Man pages for t-arae/ngscmdr

as_input_fileConvert data.frame to list of inf class object
calc_rpkmCalculate Reads Per Killobase of exon per Million mappled...
calc_rpkm_from_featurecountsCalculate RPKM from featureCounts output
calc_rpmCalculate Reads Per Million mapped reads (RPM)
calc_rpm_from_featurecountsCalculate RPM from featureCounts output
calc_tpmCalculate TPM
calc_tpm_from_featurecountsCalculate TPM from featureCounts output
cmd_getcmd_get methods for cmdopt class object
cmd_set_extract_file_from_tarExtract files from arachive file (.tar)
cmd_set_fastp_qfFilter fastq file by quality
cmd_set_merge_gzMerge some gzipped files to a gzipped file
fastqc_dataExtract information from the FastQC data.txt file
fastqc_summarySummarize FastQC summary.txt files
get_file_extGet file extensions
glue_bam_indexsamtools index
glue_bam_sortsamtools sort
glue_bamstatsamtools stats/flagstat/idxstats
glue_bowtie2_bamsortMap with bowtie2 and output a sorted bam file
glue_bowtie2_genome_generateGenerate genome index for bowtie2
glue_bowtie2_rm_contamiRemove reads from contamination with bowtie2
glue_bowtie2_rm_contami_peRemove paired end reads from contamination with bowtie2
glue_bowtie_bamsortMap with bowtie and output a sorted bam file
glue_bowtie_genome_generateGenerate genome index for bowtie
glue_check_gz_sizeCheck the decompressed file size of gzipped file
glue_cuffcomparecuffcompare commands
glue_cuffdiffcuffdiff commands
glue_cufflinkscufflinks commands
glue_cuffmergecuffmerge commands
glue_cuffnormcuffnorm commands
glue_cuffquantcuffquant commands
glue_fastp_qfFilter fastq file by quality
glue_fastp_qf_peFilter fastq file by quality
glue_fastqcCreate fastqc reports
glue_fastq_qfFilter fastq file by quality
glue_fastq_qf_clFilter fastq file by quality and Trim adaptor sequence
glue_fqgz2rfqxzconvert fastq.gz to rfq.xz
glue_genomecovCalculate genome coverage
glue_gff2bedConvert gff3 file to bed file
glue_hisat_genome_generateGenerate genome index for HISAT2
glue_pe_cutadaptClipping adaptor from pair end reads
glue_pe_featurecountsfeatureCounts for Pair-end reads
glue_pe_hisat_bamsortMap paired-end reads with hisat and output a sorted bam file
glue_pe_star_bamsortMap with STAR and output a sorted bam file
glue_rfqxz2fqgzconvert rqf.gz to fastq.gz
glue_se_cutadaptClipping adaptor from single end reads
glue_se_hisat_bamsortMap single-end reads with hisat and output a sorted bam file
glue_se_star_bamsortMap with STAR and output a sorted bam file
glue_star_genome_generateGenerate genome index for STAR
merge_featurecount_outputMerging read count tsv file from featureCounts
new_cmdoptCreate new cmdopt class object
param_generalParameters for general use
param_genomeidxParameters for genome indexing commands
pipePipe operator
pipeline_cuffdiffpipeline for cufflinks
pipeline_cuffdiff_noRABTpipeline for cufflinks
print.cmdoptPrint cmdopt class object
set_file_extSet file extensions
set_inf_classSet inf class
t-arae/ngscmdr documentation built on Sept. 23, 2019, 5:45 a.m.