API for anilchalisey/chompR
ChIP and ATAC-seq data processing pipeline

Global functions
Granges2df Man page Source code
Granges2saf Man page Source code
\%>\% Man page
align_dna Man page Source code
annotate_peaks Man page Source code
build_index Man page Source code
cc_chip Man page Source code
chain Man page
check_cmd Source code
check_sample Man page Source code
consensus_peaks Man page Source code
convert_paths Source code
create_bw Man page Source code
create_dir Source code
deseq2_analysis Man page Source code
ens2entrez Source code
ens2symbol Source code
exploratory_analysis Man page Source code
extract_numbers Source code
fl_atac Man page Source code
give_error Source code
give_note Source code
give_warning Source code
is.defined Source code
make_MA Man page Source code
make_PCA Man page Source code
make_design Source code
make_scree Man page Source code
move_file Source code
peak2Granges Man page Source code
plot_peaksummary Man page Source code
qc_alignment Man page Source code
qc_alignment2 Man page Source code
reduce_path Source code
remove_file Source code
run_atac Man page Source code
run_chip Man page Source code
run_cmd Source code
run_fastqc Man page Source code
run_featurecounts Man page Source code
run_great Man page Source code
run_hisat2 Man page Source code
run_macs2 Man page Source code
run_multiqc Man page Source code
run_sambambadup Man page Source code
run_samflagstat Man page Source code
run_samindex Man page Source code
run_samsort Man page Source code
run_samview Man page Source code
sanity_check Man page Source code
shift_bam Man page Source code
theme_publication Source code
trim_fastq Man page Source code
tss_granges Source code
anilchalisey/chompR documentation built on Sept. 28, 2018, 8:01 a.m.