inst/scripts/make-metadata.R
In dozmorovlab/preciseTADhub: Pre-trained random forest models obtained using preciseTAD
### =========================================================================
### preciseTADhub metadata
### -------------------------------------------------------------------------
###
meta <- data.frame(
Title = c("CHR1_GM12878_5kb_Arrowhead.rds",
"CHR1_GM12878_10kb_Peakachu.rds",
"CHR1_K562_5kb_Arrowhead.rds",
"CHR1_K562_10kb_Peakachu.rds",
"CHR2_GM12878_5kb_Arrowhead.rds",
"CHR2_GM12878_10kb_Peakachu.rds",
"CHR2_K562_5kb_Arrowhead.rds",
"CHR2_K562_10kb_Peakachu.rds",
"CHR3_GM12878_5kb_Arrowhead.rds",
"CHR3_GM12878_10kb_Peakachu.rds",
"CHR3_K562_5kb_Arrowhead.rds",
"CHR3_K562_10kb_Peakachu.rds",
"CHR4_GM12878_5kb_Arrowhead.rds",
"CHR4_GM12878_10kb_Peakachu.rds",
"CHR4_K562_5kb_Arrowhead.rds",
"CHR4_K562_10kb_Peakachu.rds",
"CHR5_GM12878_5kb_Arrowhead.rds",
"CHR5_GM12878_10kb_Peakachu.rds",
"CHR5_K562_5kb_Arrowhead.rds",
"CHR5_K562_10kb_Peakachu.rds",
"CHR6_GM12878_5kb_Arrowhead.rds",
"CHR6_GM12878_10kb_Peakachu.rds",
"CHR6_K562_5kb_Arrowhead.rds",
"CHR6_K562_10kb_Peakachu.rds",
"CHR7_GM12878_5kb_Arrowhead.rds",
"CHR7_GM12878_10kb_Peakachu.rds",
"CHR7_K562_5kb_Arrowhead.rds",
"CHR7_K562_10kb_Peakachu.rds",
"CHR8_GM12878_5kb_Arrowhead.rds",
"CHR8_GM12878_10kb_Peakachu.rds",
"CHR8_K562_5kb_Arrowhead.rds",
"CHR8_K562_10kb_Peakachu.rds",
"CHR10_GM12878_5kb_Arrowhead.rds",
"CHR10_GM12878_10kb_Peakachu.rds",
"CHR10_K562_5kb_Arrowhead.rds",
"CHR10_K562_10kb_Peakachu.rds",
"CHR11_GM12878_5kb_Arrowhead.rds",
"CHR11_GM12878_10kb_Peakachu.rds",
"CHR11_K562_5kb_Arrowhead.rds",
"CHR11_K562_10kb_Peakachu.rds",
"CHR12_GM12878_5kb_Arrowhead.rds",
"CHR12_GM12878_10kb_Peakachu.rds",
"CHR12_K562_5kb_Arrowhead.rds",
"CHR12_K562_10kb_Peakachu.rds",
"CHR13_GM12878_5kb_Arrowhead.rds",
"CHR13_GM12878_10kb_Peakachu.rds",
"CHR13_K562_5kb_Arrowhead.rds",
"CHR13_K562_10kb_Peakachu.rds",
"CHR14_GM12878_5kb_Arrowhead.rds",
"CHR14_GM12878_10kb_Peakachu.rds",
"CHR14_K562_5kb_Arrowhead.rds",
"CHR14_K562_10kb_Peakachu.rds",
"CHR15_GM12878_5kb_Arrowhead.rds",
"CHR15_GM12878_10kb_Peakachu.rds",
"CHR15_K562_5kb_Arrowhead.rds",
"CHR15_K562_10kb_Peakachu.rds",
"CHR16_GM12878_5kb_Arrowhead.rds",
"CHR16_GM12878_10kb_Peakachu.rds",
"CHR16_K562_5kb_Arrowhead.rds",
"CHR16_K562_10kb_Peakachu.rds",
"CHR17_GM12878_5kb_Arrowhead.rds",
"CHR17_GM12878_10kb_Peakachu.rds",
"CHR17_K562_5kb_Arrowhead.rds",
"CHR17_K562_10kb_Peakachu.rds",
"CHR18_GM12878_5kb_Arrowhead.rds",
"CHR18_GM12878_10kb_Peakachu.rds",
"CHR18_K562_5kb_Arrowhead.rds",
"CHR18_K562_10kb_Peakachu.rds",
"CHR19_GM12878_5kb_Arrowhead.rds",
"CHR19_GM12878_10kb_Peakachu.rds",
"CHR19_K562_5kb_Arrowhead.rds",
"CHR19_K562_10kb_Peakachu.rds",
"CHR20_GM12878_5kb_Arrowhead.rds",
"CHR20_GM12878_10kb_Peakachu.rds",
"CHR20_K562_5kb_Arrowhead.rds",
"CHR20_K562_10kb_Peakachu.rds",
"CHR21_GM12878_5kb_Arrowhead.rds",
"CHR21_GM12878_10kb_Peakachu.rds",
"CHR21_K562_5kb_Arrowhead.rds",
"CHR21_K562_10kb_Peakachu.rds",
"CHR22_GM12878_5kb_Arrowhead.rds",
"CHR22_GM12878_10kb_Peakachu.rds",
"CHR22_K562_5kb_Arrowhead.rds",
"CHR22_K562_10kb_Peakachu.rds"),
Description = c("Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR1 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR1 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR1 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR1 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR2 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR2 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR2 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR2 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR3 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR3 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR3 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR3 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR4 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR4 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR4 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR4 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR5 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR5 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR5 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR5 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR6 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR6 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR6 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR6 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR7 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR7 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR7 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR7 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR8 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR8 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR8 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR8 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR10 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR10 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR10 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR10 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR11 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR11 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR11 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR11 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR12 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR12 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR12 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR12 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR13 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR13 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR13 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR13 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR14 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR14 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR14 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR14 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR15 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR15 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR15 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR15 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR16 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR16 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR16 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR16 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR17 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR17 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR17 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR17 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR18 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR18 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR18 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR18 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR19 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR19 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR19 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR19 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR20 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR20 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR20 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR20 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR21 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR21 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR21 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR21 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR22 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR22 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR22 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR22 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562"),
BiocVersion = c(rep("3.12", 84)),
Genome = c(rep("hg19", 84)),
SourceType = c(rep("RDS", 84)),
SourceUrl = "https://onedrive.live.com/?authkey=%21AEdP2%5FgyT%5FY0zSs&id=5BE46CBE2B039B19%2146565&cid=5BE46CBE2B039B19",
SourceVersion = "Oct 16 2020",
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "preciseTAD",
Maintainer = "Mikhail Dozmorov <mikhail.dozmorov@vcuhealth.org>",
RDataClass = c(rep("list", 84)),
DispatchClass = c(rep("Rds",84)),
RDataPath = c("preciseTADhub/CHR1_GM12878_5kb_Arrowhead.rds",
"preciseTADhub/CHR1_GM12878_10kb_Peakachu.rds",
"preciseTADhub/CHR1_K562_5kb_Arrowhead.rds",
"preciseTADhub/CHR1_K562_10kb_Peakachu.rds",
"preciseTADhub/CHR2_GM12878_5kb_Arrowhead.rds",
"preciseTADhub/CHR2_GM12878_10kb_Peakachu.rds",
"preciseTADhub/CHR2_K562_5kb_Arrowhead.rds",
"preciseTADhub/CHR2_K562_10kb_Peakachu.rds",
"preciseTADhub/CHR3_GM12878_5kb_Arrowhead.rds",
"preciseTADhub/CHR3_GM12878_10kb_Peakachu.rds",
"preciseTADhub/CHR3_K562_5kb_Arrowhead.rds",
"preciseTADhub/CHR3_K562_10kb_Peakachu.rds",
"preciseTADhub/CHR4_GM12878_5kb_Arrowhead.rds",
"preciseTADhub/CHR4_GM12878_10kb_Peakachu.rds",
"preciseTADhub/CHR4_K562_5kb_Arrowhead.rds",
"preciseTADhub/CHR4_K562_10kb_Peakachu.rds",
"preciseTADhub/CHR5_GM12878_5kb_Arrowhead.rds",
"preciseTADhub/CHR5_GM12878_10kb_Peakachu.rds",
"preciseTADhub/CHR5_K562_5kb_Arrowhead.rds",
"preciseTADhub/CHR5_K562_10kb_Peakachu.rds",
"preciseTADhub/CHR6_GM12878_5kb_Arrowhead.rds",
"preciseTADhub/CHR6_GM12878_10kb_Peakachu.rds",
"preciseTADhub/CHR6_K562_5kb_Arrowhead.rds",
"preciseTADhub/CHR6_K562_10kb_Peakachu.rds",
"preciseTADhub/CHR7_GM12878_5kb_Arrowhead.rds",
"preciseTADhub/CHR7_GM12878_10kb_Peakachu.rds",
"preciseTADhub/CHR7_K562_5kb_Arrowhead.rds",
"preciseTADhub/CHR7_K562_10kb_Peakachu.rds",
"preciseTADhub/CHR8_GM12878_5kb_Arrowhead.rds",
"preciseTADhub/CHR8_GM12878_10kb_Peakachu.rds",
"preciseTADhub/CHR8_K562_5kb_Arrowhead.rds",
"preciseTADhub/CHR8_K562_10kb_Peakachu.rds",
"preciseTADhub/CHR10_GM12878_5kb_Arrowhead.rds",
"preciseTADhub/CHR10_GM12878_10kb_Peakachu.rds",
"preciseTADhub/CHR10_K562_5kb_Arrowhead.rds",
"preciseTADhub/CHR10_K562_10kb_Peakachu.rds",
"preciseTADhub/CHR11_GM12878_5kb_Arrowhead.rds",
"preciseTADhub/CHR11_GM12878_10kb_Peakachu.rds",
"preciseTADhub/CHR11_K562_5kb_Arrowhead.rds",
"preciseTADhub/CHR11_K562_10kb_Peakachu.rds",
"preciseTADhub/CHR12_GM12878_5kb_Arrowhead.rds",
"preciseTADhub/CHR12_GM12878_10kb_Peakachu.rds",
"preciseTADhub/CHR12_K562_5kb_Arrowhead.rds",
"preciseTADhub/CHR12_K562_10kb_Peakachu.rds",
"preciseTADhub/CHR13_GM12878_5kb_Arrowhead.rds",
"preciseTADhub/CHR13_GM12878_10kb_Peakachu.rds",
"preciseTADhub/CHR13_K562_5kb_Arrowhead.rds",
"preciseTADhub/CHR13_K562_10kb_Peakachu.rds",
"preciseTADhub/CHR14_GM12878_5kb_Arrowhead.rds",
"preciseTADhub/CHR14_GM12878_10kb_Peakachu.rds",
"preciseTADhub/CHR14_K562_5kb_Arrowhead.rds",
"preciseTADhub/CHR14_K562_10kb_Peakachu.rds",
"preciseTADhub/CHR15_GM12878_5kb_Arrowhead.rds",
"preciseTADhub/CHR15_GM12878_10kb_Peakachu.rds",
"preciseTADhub/CHR15_K562_5kb_Arrowhead.rds",
"preciseTADhub/CHR15_K562_10kb_Peakachu.rds",
"preciseTADhub/CHR16_GM12878_5kb_Arrowhead.rds",
"preciseTADhub/CHR16_GM12878_10kb_Peakachu.rds",
"preciseTADhub/CHR16_K562_5kb_Arrowhead.rds",
"preciseTADhub/CHR16_K562_10kb_Peakachu.rds",
"preciseTADhub/CHR17_GM12878_5kb_Arrowhead.rds",
"preciseTADhub/CHR17_GM12878_10kb_Peakachu.rds",
"preciseTADhub/CHR17_K562_5kb_Arrowhead.rds",
"preciseTADhub/CHR17_K562_10kb_Peakachu.rds",
"preciseTADhub/CHR18_GM12878_5kb_Arrowhead.rds",
"preciseTADhub/CHR18_GM12878_10kb_Peakachu.rds",
"preciseTADhub/CHR18_K562_5kb_Arrowhead.rds",
"preciseTADhub/CHR18_K562_10kb_Peakachu.rds",
"preciseTADhub/CHR19_GM12878_5kb_Arrowhead.rds",
"preciseTADhub/CHR19_GM12878_10kb_Peakachu.rds",
"preciseTADhub/CHR19_K562_5kb_Arrowhead.rds",
"preciseTADhub/CHR19_K562_10kb_Peakachu.rds",
"preciseTADhub/CHR20_GM12878_5kb_Arrowhead.rds",
"preciseTADhub/CHR20_GM12878_10kb_Peakachu.rds",
"preciseTADhub/CHR20_K562_5kb_Arrowhead.rds",
"preciseTADhub/CHR20_K562_10kb_Peakachu.rds",
"preciseTADhub/CHR21_GM12878_5kb_Arrowhead.rds",
"preciseTADhub/CHR21_GM12878_10kb_Peakachu.rds",
"preciseTADhub/CHR21_K562_5kb_Arrowhead.rds",
"preciseTADhub/CHR21_K562_10kb_Peakachu.rds",
"preciseTADhub/CHR22_GM12878_5kb_Arrowhead.rds",
"preciseTADhub/CHR22_GM12878_10kb_Peakachu.rds",
"preciseTADhub/CHR22_K562_5kb_Arrowhead.rds",
"preciseTADhub/CHR22_K562_10kb_Peakachu.rds"),
Tags = "",
Notes = "")
write.csv(meta, file="inst/extdata/metadata.csv", row.names=FALSE)
dozmorovlab/preciseTADhub documentation built on Aug. 14, 2021, 8:19 p.m.
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### =========================================================================
### preciseTADhub metadata
### -------------------------------------------------------------------------
###
meta <- data.frame(
Title = c("CHR1_GM12878_5kb_Arrowhead.rds",
"CHR1_GM12878_10kb_Peakachu.rds",
"CHR1_K562_5kb_Arrowhead.rds",
"CHR1_K562_10kb_Peakachu.rds",
"CHR2_GM12878_5kb_Arrowhead.rds",
"CHR2_GM12878_10kb_Peakachu.rds",
"CHR2_K562_5kb_Arrowhead.rds",
"CHR2_K562_10kb_Peakachu.rds",
"CHR3_GM12878_5kb_Arrowhead.rds",
"CHR3_GM12878_10kb_Peakachu.rds",
"CHR3_K562_5kb_Arrowhead.rds",
"CHR3_K562_10kb_Peakachu.rds",
"CHR4_GM12878_5kb_Arrowhead.rds",
"CHR4_GM12878_10kb_Peakachu.rds",
"CHR4_K562_5kb_Arrowhead.rds",
"CHR4_K562_10kb_Peakachu.rds",
"CHR5_GM12878_5kb_Arrowhead.rds",
"CHR5_GM12878_10kb_Peakachu.rds",
"CHR5_K562_5kb_Arrowhead.rds",
"CHR5_K562_10kb_Peakachu.rds",
"CHR6_GM12878_5kb_Arrowhead.rds",
"CHR6_GM12878_10kb_Peakachu.rds",
"CHR6_K562_5kb_Arrowhead.rds",
"CHR6_K562_10kb_Peakachu.rds",
"CHR7_GM12878_5kb_Arrowhead.rds",
"CHR7_GM12878_10kb_Peakachu.rds",
"CHR7_K562_5kb_Arrowhead.rds",
"CHR7_K562_10kb_Peakachu.rds",
"CHR8_GM12878_5kb_Arrowhead.rds",
"CHR8_GM12878_10kb_Peakachu.rds",
"CHR8_K562_5kb_Arrowhead.rds",
"CHR8_K562_10kb_Peakachu.rds",
"CHR10_GM12878_5kb_Arrowhead.rds",
"CHR10_GM12878_10kb_Peakachu.rds",
"CHR10_K562_5kb_Arrowhead.rds",
"CHR10_K562_10kb_Peakachu.rds",
"CHR11_GM12878_5kb_Arrowhead.rds",
"CHR11_GM12878_10kb_Peakachu.rds",
"CHR11_K562_5kb_Arrowhead.rds",
"CHR11_K562_10kb_Peakachu.rds",
"CHR12_GM12878_5kb_Arrowhead.rds",
"CHR12_GM12878_10kb_Peakachu.rds",
"CHR12_K562_5kb_Arrowhead.rds",
"CHR12_K562_10kb_Peakachu.rds",
"CHR13_GM12878_5kb_Arrowhead.rds",
"CHR13_GM12878_10kb_Peakachu.rds",
"CHR13_K562_5kb_Arrowhead.rds",
"CHR13_K562_10kb_Peakachu.rds",
"CHR14_GM12878_5kb_Arrowhead.rds",
"CHR14_GM12878_10kb_Peakachu.rds",
"CHR14_K562_5kb_Arrowhead.rds",
"CHR14_K562_10kb_Peakachu.rds",
"CHR15_GM12878_5kb_Arrowhead.rds",
"CHR15_GM12878_10kb_Peakachu.rds",
"CHR15_K562_5kb_Arrowhead.rds",
"CHR15_K562_10kb_Peakachu.rds",
"CHR16_GM12878_5kb_Arrowhead.rds",
"CHR16_GM12878_10kb_Peakachu.rds",
"CHR16_K562_5kb_Arrowhead.rds",
"CHR16_K562_10kb_Peakachu.rds",
"CHR17_GM12878_5kb_Arrowhead.rds",
"CHR17_GM12878_10kb_Peakachu.rds",
"CHR17_K562_5kb_Arrowhead.rds",
"CHR17_K562_10kb_Peakachu.rds",
"CHR18_GM12878_5kb_Arrowhead.rds",
"CHR18_GM12878_10kb_Peakachu.rds",
"CHR18_K562_5kb_Arrowhead.rds",
"CHR18_K562_10kb_Peakachu.rds",
"CHR19_GM12878_5kb_Arrowhead.rds",
"CHR19_GM12878_10kb_Peakachu.rds",
"CHR19_K562_5kb_Arrowhead.rds",
"CHR19_K562_10kb_Peakachu.rds",
"CHR20_GM12878_5kb_Arrowhead.rds",
"CHR20_GM12878_10kb_Peakachu.rds",
"CHR20_K562_5kb_Arrowhead.rds",
"CHR20_K562_10kb_Peakachu.rds",
"CHR21_GM12878_5kb_Arrowhead.rds",
"CHR21_GM12878_10kb_Peakachu.rds",
"CHR21_K562_5kb_Arrowhead.rds",
"CHR21_K562_10kb_Peakachu.rds",
"CHR22_GM12878_5kb_Arrowhead.rds",
"CHR22_GM12878_10kb_Peakachu.rds",
"CHR22_K562_5kb_Arrowhead.rds",
"CHR22_K562_10kb_Peakachu.rds"),
Description = c("Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR1 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR1 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR1 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR1 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR2 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR2 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR2 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR2 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR3 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR3 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR3 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR3 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR4 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR4 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR4 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR4 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR5 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR5 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR5 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR5 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR6 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR6 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR6 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR6 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR7 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR7 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR7 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR7 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR8 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR8 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR8 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR8 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR10 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR10 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR10 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR10 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR11 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR11 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR11 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR11 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR12 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR12 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR12 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR12 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR13 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR13 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR13 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR13 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR14 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR14 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR14 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR14 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR15 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR15 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR15 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR15 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR16 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR16 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR16 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR16 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR17 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR17 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR17 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR17 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR18 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR18 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR18 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR18 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR19 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR19 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR19 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR19 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR20 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR20 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR20 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR20 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR21 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR21 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR21 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR21 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR22 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR22 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for GM12878",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR22 as a holdout chromosome, Arrowhead ground truth TAD boundaries, at 5 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562",
"Pre-trained model built using TADrandomForest from the preciseTAD R package with CHR22 as a holdout chromosome, Peakachu ground truth TAD boundaries, at 10 kb resolution, with random under-sampling, and distance-type features from CTCF, RAD21, SMC3, and ZNF143 ChIP-seq peaks for K562"),
BiocVersion = c(rep("3.12", 84)),
Genome = c(rep("hg19", 84)),
SourceType = c(rep("RDS", 84)),
SourceUrl = "https://onedrive.live.com/?authkey=%21AEdP2%5FgyT%5FY0zSs&id=5BE46CBE2B039B19%2146565&cid=5BE46CBE2B039B19",
SourceVersion = "Oct 16 2020",
Species = "Homo sapiens",
TaxonomyId = 9606,
Coordinate_1_based = TRUE,
DataProvider = "preciseTAD",
Maintainer = "Mikhail Dozmorov <mikhail.dozmorov@vcuhealth.org>",
RDataClass = c(rep("list", 84)),
DispatchClass = c(rep("Rds",84)),
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"preciseTADhub/CHR10_GM12878_5kb_Arrowhead.rds",
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"preciseTADhub/CHR13_GM12878_5kb_Arrowhead.rds",
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"preciseTADhub/CHR18_GM12878_5kb_Arrowhead.rds",
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"preciseTADhub/CHR19_GM12878_5kb_Arrowhead.rds",
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"preciseTADhub/CHR20_GM12878_5kb_Arrowhead.rds",
"preciseTADhub/CHR20_GM12878_10kb_Peakachu.rds",
"preciseTADhub/CHR20_K562_5kb_Arrowhead.rds",
"preciseTADhub/CHR20_K562_10kb_Peakachu.rds",
"preciseTADhub/CHR21_GM12878_5kb_Arrowhead.rds",
"preciseTADhub/CHR21_GM12878_10kb_Peakachu.rds",
"preciseTADhub/CHR21_K562_5kb_Arrowhead.rds",
"preciseTADhub/CHR21_K562_10kb_Peakachu.rds",
"preciseTADhub/CHR22_GM12878_5kb_Arrowhead.rds",
"preciseTADhub/CHR22_GM12878_10kb_Peakachu.rds",
"preciseTADhub/CHR22_K562_5kb_Arrowhead.rds",
"preciseTADhub/CHR22_K562_10kb_Peakachu.rds"),
Tags = "",
Notes = "")
write.csv(meta, file="inst/extdata/metadata.csv", row.names=FALSE)
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