Files in Jeremy37/rgenie
Analysis of GenIE Experiments
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
R/data.R
R/genie_functions.R
R/plots.R
R/read_experiment.R
README.md
data/atac_del_results.rda
data/atac_grep_results.rda
data/atac_regions.rda
data/atac_replicates.rda
data/mul1_del_results.rda
data/mul1_grep_results.rda
data/mul1_regions.rda
data/mul1_replicates.rda
example_data/ATAC_rs7729529/rs7729529.genie_regions.tsv
example_data/ATAC_rs7729529/rs7729529.genie_replicates.tsv
example_data/ATAC_rs7729529/rs7729529_atac1_pcr1.sortedByCoord.bam
example_data/ATAC_rs7729529/rs7729529_atac1_pcr1.sortedByCoord.bam.bai
example_data/ATAC_rs7729529/rs7729529_atac1_pcr2.sortedByCoord.bam
example_data/ATAC_rs7729529/rs7729529_atac1_pcr2.sortedByCoord.bam.bai
example_data/ATAC_rs7729529/rs7729529_atac1_pcr3.sortedByCoord.bam
example_data/ATAC_rs7729529/rs7729529_atac1_pcr3.sortedByCoord.bam.bai
example_data/ATAC_rs7729529/rs7729529_gDNA1_pcr1.sortedByCoord.bam
example_data/ATAC_rs7729529/rs7729529_gDNA1_pcr1.sortedByCoord.bam.bai
example_data/ATAC_rs7729529/rs7729529_gDNA1_pcr2.sortedByCoord.bam
example_data/ATAC_rs7729529/rs7729529_gDNA1_pcr2.sortedByCoord.bam.bai
example_data/ATAC_rs7729529/rs7729529_gDNA1_pcr3.sortedByCoord.bam
example_data/ATAC_rs7729529/rs7729529_gDNA1_pcr3.sortedByCoord.bam.bai
example_data/MUL1/MUL1.genie_regions.tsv
example_data/MUL1/MUL1.genie_replicates.tsv
example_data/MUL1/MUL1_rs6700034_cDNA_rep1_pcr1.sortedByCoord.bam
example_data/MUL1/MUL1_rs6700034_cDNA_rep1_pcr1.sortedByCoord.bam.bai
example_data/MUL1/MUL1_rs6700034_cDNA_rep1_pcr2.sortedByCoord.bam
example_data/MUL1/MUL1_rs6700034_cDNA_rep1_pcr2.sortedByCoord.bam.bai
example_data/MUL1/MUL1_rs6700034_cDNA_rep1_pcr3.sortedByCoord.bam
example_data/MUL1/MUL1_rs6700034_cDNA_rep1_pcr3.sortedByCoord.bam.bai
example_data/MUL1/MUL1_rs6700034_cDNA_rep1_pcr4.sortedByCoord.bam
example_data/MUL1/MUL1_rs6700034_cDNA_rep1_pcr4.sortedByCoord.bam.bai
example_data/MUL1/MUL1_rs6700034_cDNA_rep2_pcr5.sortedByCoord.bam
example_data/MUL1/MUL1_rs6700034_cDNA_rep2_pcr5.sortedByCoord.bam.bai
example_data/MUL1/MUL1_rs6700034_cDNA_rep2_pcr6.sortedByCoord.bam
example_data/MUL1/MUL1_rs6700034_cDNA_rep2_pcr6.sortedByCoord.bam.bai
example_data/MUL1/MUL1_rs6700034_cDNA_rep2_pcr7.sortedByCoord.bam
example_data/MUL1/MUL1_rs6700034_cDNA_rep2_pcr7.sortedByCoord.bam.bai
example_data/MUL1/MUL1_rs6700034_cDNA_rep2_pcr8.sortedByCoord.bam
example_data/MUL1/MUL1_rs6700034_cDNA_rep2_pcr8.sortedByCoord.bam.bai
example_data/MUL1/MUL1_rs6700034_gDNA_rep1_pcr1.sortedByCoord.bam
example_data/MUL1/MUL1_rs6700034_gDNA_rep1_pcr1.sortedByCoord.bam.bai
example_data/MUL1/MUL1_rs6700034_gDNA_rep1_pcr2.sortedByCoord.bam
example_data/MUL1/MUL1_rs6700034_gDNA_rep1_pcr2.sortedByCoord.bam.bai
example_data/MUL1/MUL1_rs6700034_gDNA_rep1_pcr3.sortedByCoord.bam
example_data/MUL1/MUL1_rs6700034_gDNA_rep1_pcr3.sortedByCoord.bam.bai
example_data/MUL1/MUL1_rs6700034_gDNA_rep1_pcr4.sortedByCoord.bam
example_data/MUL1/MUL1_rs6700034_gDNA_rep1_pcr4.sortedByCoord.bam.bai
example_data/deletion_alleles_plot.png
example_data/file_list.ATAC_rs7729529.txt
example_data/file_list.MUL1.txt
inst/CITATION
man/aligned_read_profile_plots.Rd
man/alignment_analysis.Rd
man/alignment_analysis_plots.Rd
man/alignment_summary_plot.Rd
man/allele_effect_plot.Rd
man/atac_del_results.Rd
man/atac_grep_results.Rd
man/atac_regions.Rd
man/atac_replicates.Rd
man/bind_results.Rd
man/deletion_alleles_plot.Rd
man/deletion_profile_plot.Rd
man/download_example.Rd
man/experiment_summary_plot.Rd
man/genie_plot_options.Rd
man/get_variance_components.Rd
man/grep_analysis.Rd
man/grep_summary_plot.Rd
man/mul1_del_results.Rd
man/mul1_grep_results.Rd
man/mul1_regions.Rd
man/mul1_replicates.Rd
man/power_analysis.Rd
man/power_plots.Rd
man/replicate_qc_plot.Rd
man/replicate_summary_plot.Rd
man/rgenie.Rd
man/variance_components_plot.Rd
man/write_results.Rd
vignettes/.gitignore
vignettes/advanced_rgenie.Rmd
vignettes/advanced_rgenie.html
vignettes/introduction.Rmd
vignettes/introduction.html
vignettes/rgenie_atac.Rmd
vignettes/rgenie_atac.html
