Files in anilchalisey/chompR
ChIP and ATAC-seq data processing pipeline

.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
NEWS.md R/align_dna.R R/annotate_peaks.R R/build_index.R R/cc_chip.R R/chain.R R/check_sample.R R/consensus_peaks.R R/convert_files.R R/create_bw.R R/deseq2_analysis.R R/exploratory_analysis.R R/fl_atac.R R/make_MA.R R/make_PCA.R R/make_scree.R R/plot_peaksummary.R R/qc_alignment.R R/qc_alignment2.R R/run_atac.R R/run_chip.R R/run_fastqc.R R/run_featurecounts.R R/run_great.R R/run_hisat2.R R/run_macs2.R R/run_multiqc.R R/run_sambamba.R R/run_samtools.R R/sanity_check.R R/shift_bam.R R/trim_fastq.R R/utils-pipe.R R/utils.R README.Rmd README.md
_pkgdown.yml
chompR.Rproj
data/chain.rda
docs/LICENSE-text.html
docs/_config.yml
docs/authors.html
docs/docsearch.css
docs/docsearch.js
docs/favicon.ico
docs/index.html
docs/link.svg
docs/logo.png
docs/news/index.html
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/align_dna.html
docs/reference/annotate_peaks.html
docs/reference/build_index.html
docs/reference/cc_chip.html
docs/reference/chain.html
docs/reference/check_sample.html
docs/reference/consensus_peaks.html
docs/reference/create_bw.html
docs/reference/deseq2_analysis.html
docs/reference/exploratory_analysis.html
docs/reference/figures/logo.png
docs/reference/fl_atac.html
docs/reference/index.html
docs/reference/make_MA.html
docs/reference/make_PCA.html
docs/reference/make_scree.html
docs/reference/peak2Granges.html
docs/reference/pipe.html
docs/reference/plot_peaksummary.html
docs/reference/qc_alignment.html
docs/reference/qc_alignment2.html
docs/reference/run_atac.html
docs/reference/run_chip.html
docs/reference/run_fastqc.html
docs/reference/run_featurecounts.html
docs/reference/run_great.html
docs/reference/run_hisat2.html
docs/reference/run_macs2.html
docs/reference/run_multiqc.html
docs/reference/run_sambambadup.html
docs/reference/run_samsort.html
docs/reference/sanity_check.html
docs/reference/shift_bam.html
docs/reference/trim_fastq.html
docs/sitemap.xml
inst/extdata/MULTIQC/Logo.png
inst/extdata/MULTIQC/multiqc_config.yaml
inst/extdata/paired-example.txt
inst/extdata/single-example.txt
inst/src/pyadapter_trim.py
inst/src/readLength.sh
man/align_dna.Rd man/annotate_peaks.Rd man/build_index.Rd man/cc_chip.Rd man/chain.Rd man/check_sample.Rd man/consensus_peaks.Rd man/create_bw.Rd man/deseq2_analysis.Rd man/exploratory_analysis.Rd
man/figures/logo.png
man/fl_atac.Rd man/make_MA.Rd man/make_PCA.Rd man/make_scree.Rd man/peak2Granges.Rd man/pipe.Rd man/plot_peaksummary.Rd man/qc_alignment.Rd man/qc_alignment2.Rd man/run_atac.Rd man/run_chip.Rd man/run_fastqc.Rd man/run_featurecounts.Rd man/run_great.Rd man/run_hisat2.Rd man/run_macs2.Rd man/run_multiqc.Rd man/run_sambambadup.Rd man/run_samsort.Rd man/sanity_check.Rd man/shift_bam.Rd man/trim_fastq.Rd
anilchalisey/chompR documentation built on Sept. 28, 2018, 8:01 a.m.