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 May 9, 2019, 3:59 a.m.