Files in flow-r/ngsflows
Robust Pipelines for Next-Generation Sequencing Analysis; A Companion Package for flowr
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
NEWS.md
R/annotate.R
R/bwa.R
R/chipseq.R
R/depthofcoverage.R
R/fastqc.R
R/fetch_genomes.R
R/freebayes.R
R/generic.R
R/haplotyper.R
R/modules.R
R/mut2maf.R
R/mutect.R
R/parse_vcf.R
R/picard.R
R/preprocess.R
R/samblaster.R
R/samtools.R
R/scripture.R
R/sheets_fastqs.R
R/split_fq.R
R/star.R
R/zzz.R
README.html
README.rmd
contributing.md
inst/conf/ngsflows.conf
inst/conf/ngsflows_mda.conf
inst/pipelines/bam_preprocess.R
inst/pipelines/bam_preprocess.def
inst/pipelines/bam_preprocess.pdf
inst/pipelines/fastq_bam_bwa.conf
inst/pipelines/fastq_haplotyper.R
inst/pipelines/fastq_haplotyper.conf
inst/pipelines/fastq_haplotyper.def
inst/pipelines/fastq_haplotyper.pdf
inst/scripts/count_fastq_indexes.sh
inst/scripts/fastq-splitter.pl
inst/scripts/somatic_filter.sh
inst/scripts/split_fq
inst/scripts/split_fq.py
inst/scripts/split_fq.sh
man/annotate.Rd
man/annotate_mutect.Rd
man/annotate_variants.Rd
man/annotate_vcf.Rd
man/avail_genomes.Rd
man/bwa.Rd
man/check_fastq_sheet.Rd
man/chipseq.Rd
man/chk_fq.Rd
man/create_fq_sheet.Rd
man/create_sample_sheet.Rd
man/fastqc.Rd
man/fetch_genomes.Rd
man/get_fasta_chrs.Rd
man/get_fq_ext.Rd
man/haplotyper.Rd
man/merge_sheets.Rd
man/modules.Rd
man/mutect.Rd
man/parse_somatic_vcf.Rd
man/parse_vcf.Rd
man/picard_bam_fastq.Rd
man/picard_merge.Rd
man/picard_reorder.Rd
man/picard_rg.Rd
man/preprocess.Rd
man/samtools.Rd
man/split_fq.Rd
man/split_names_fastq.Rd
man/split_names_fastq2.Rd
man/star.Rd
man/star_index.Rd
ngflows.Rproj
notes.Rmd
vignettes/module_list.Rmd
