Files in trichelab/spiky
Spike-in calibration for cell-free MeDIP
.Rbuildignore
.Rinstignore
.gitignore
.travis.yml
DESCRIPTION
Makefile
NAMESPACE
NEWS.md
R/add_frag_info.R
R/bam_to_bins.R
R/bin_pmol.R
R/convertPairedGRtoGR.R
R/covg_to_df.R
R/data.R
R/find_spike_contigs.R
R/generate_spike_fasta.R
R/generics.R
R/get_base_name.R
R/get_binned_coverage.R
R/get_merged_gr.R
R/get_spike_depth.R
R/get_spiked_coverage.R
R/kmax.R
R/kmers.R
R/methylation_specificity.R
R/model_bam_standards.R
R/model_glm_pmol.R
R/parse_spike_UMI.R
R/predict_pmol.R
R/process_spikes.R
R/read_bedpe.R
R/rename_spike_seqlevels.R
R/rename_spikes.R
R/scan_genomic_bedpe.R
R/scan_genomic_contigs.R
R/scan_methylation_specificity.R
R/scan_spike_bedpe.R
R/scan_spike_contigs.R
R/scan_spike_counts.R
R/scan_spiked_bam.R
R/seqinfo_from_header.R
R/spike_bland_altman_plot.R
R/spike_counts.R
R/tile_bins.R
README.md
data/dedup.rda
data/genbank_mito.rda
data/genomic_res.rda
data/phage.rda
data/spike.rda
data/spike_cram_counts.rda
data/spike_read_counts.rda
data/spike_res.rda
data/ssb_res.rda
data/testGR.rda
inst/extdata/2020_Human0.01_test.csv.gz
inst/extdata/2020_dedup_spikein_data.csv.gz
inst/extdata/GSM5067067_2020_6654_bedpe.bam
inst/extdata/cfMeDIPspikes.fa
inst/extdata/example.spike.bam
inst/extdata/example.spike.bam.bai
inst/extdata/example_chr21.bam
inst/extdata/example_chr21.bam.bai
inst/extdata/example_chr21_bedpe.bed.gz
inst/extdata/example_chr21_bedpe.bed.gz.tbi
inst/extdata/example_spike_bedpe.bed.gz
inst/extdata/example_spike_bedpe.bed.gz.tbi
inst/extdata/phages.fa
inst/extdata/spike_contigs.fa
inst/extdata/spikes.fa
inst/script/genbank_mito.R
inst/script/loadDedup.R
inst/script/loadTest.R
inst/script/mergeBeds.R
man/add_frag_info.Rd
man/bam_to_bins.Rd
man/bin_pmol.Rd
man/convertPairedGRtoGR.Rd
man/covg_to_df.Rd
man/dedup.Rd
man/find_spike_contigs.Rd
man/genbank_mito.Rd
man/generate_spike_fasta.Rd
man/genomic_res.Rd
man/get_base_name.Rd
man/get_binned_coverage.Rd
man/get_merged_gr.Rd
man/get_spike_depth.Rd
man/get_spiked_coverage.Rd
man/kmax.Rd
man/kmers.Rd
man/methylation_specificity.Rd
man/model_bam_standards.Rd
man/model_glm_pmol.Rd
man/parse_spike_UMI.Rd
man/phage.Rd
man/predict_pmol.Rd
man/process_spikes.Rd
man/read_bedpe.Rd
man/rename_spike_seqlevels.Rd
man/rename_spikes.Rd
man/scan_genomic_bedpe.Rd
man/scan_genomic_contigs.Rd
man/scan_methylation_specificity.Rd
man/scan_spike_bedpe.Rd
man/scan_spike_contigs.Rd
man/scan_spike_counts.Rd
man/scan_spiked_bam.Rd
man/seqinfo_from_header.Rd
man/spike.Rd
man/spike_bland_altman_plot.Rd
man/spike_counts.Rd
man/spike_cram_counts.Rd
man/spike_read_counts.Rd
man/spike_res.Rd
man/spiky-methods.Rd
man/ssb_res.Rd
man/testGR.Rd
man/tile_bins.Rd
vignettes/.gitignore
vignettes/nature.csl
vignettes/references.bib
vignettes/spiky-small.png
vignettes/spiky_vignette.Rmd
