Man pages for t-arae/ngscmdr
| as_input_file | Convert data.frame to list of inf class object |
| calc_rpkm | Calculate Reads Per Killobase of exon per Million mappled... |
| calc_rpkm_from_featurecounts | Calculate RPKM from featureCounts output |
| calc_rpm | Calculate Reads Per Million mapped reads (RPM) |
| calc_rpm_from_featurecounts | Calculate RPM from featureCounts output |
| calc_tpm | Calculate TPM |
| calc_tpm_from_featurecounts | Calculate TPM from featureCounts output |
| cmd_get | cmd_get methods for cmdopt class object |
| cmd_set_extract_file_from_tar | Extract files from arachive file (.tar) |
| cmd_set_fastp_qf | Filter fastq file by quality |
| cmd_set_merge_gz | Merge some gzipped files to a gzipped file |
| fastqc_data | Extract information from the FastQC data.txt file |
| fastqc_summary | Summarize FastQC summary.txt files |
| get_file_ext | Get file extensions |
| glue_bam2wig | bam2wig.py |
| glue_bam_index | samtools index |
| glue_bam_sort | samtools sort |
| glue_bamstat | samtools stats/flagstat/idxstats |
| glue_bowtie2_bamsort | Map with bowtie2 and output a sorted bam file |
| glue_bowtie2_genome_generate | Generate genome index for bowtie2 |
| glue_bowtie2_rm_contami | Remove reads from contamination with bowtie2 |
| glue_bowtie2_rm_contami_pe | Remove paired end reads from contamination with bowtie2 |
| glue_bowtie_bamsort | Map with bowtie and output a sorted bam file |
| glue_bowtie_genome_generate | Generate genome index for bowtie |
| glue_check_gz_size | Check the decompressed file size of gzipped file |
| glue_cuffcompare | cuffcompare commands |
| glue_cuffdiff | cuffdiff commands |
| glue_cufflinks | cufflinks commands |
| glue_cuffmerge | cuffmerge commands |
| glue_cuffnorm | cuffnorm commands |
| glue_cuffquant | cuffquant commands |
| glue_fastp_qf | Filter fastq file by quality |
| glue_fastp_qf_pe | Filter fastq file by quality |
| glue_fastqc | Create fastqc reports |
| glue_fastq_qf | Filter fastq file by quality |
| glue_fastq_qf_cl | Filter fastq file by quality and Trim adaptor sequence |
| glue_fqgz2rfqxz | convert fastq.gz to rfq.xz |
| glue_genomecov | Calculate genome coverage |
| glue_gff2bed | Convert gff3 file to bed file |
| glue_hisat_genome_generate | Generate genome index for HISAT2 |
| glue_pe_cutadapt | Clipping adaptor from pair end reads |
| glue_pe_featurecounts | featureCounts for Pair-end reads |
| glue_pe_hisat_bamsort | Map paired-end reads with hisat and output a sorted bam file |
| glue_pe_star_bamsort | Map with STAR and output a sorted bam file |
| glue_rfqxz2fqgz | convert rqf.gz to fastq.gz |
| glue_se_cutadapt | Clipping adaptor from single end reads |
| glue_se_featurecounts | featureCounts |
| glue_se_hisat_bamsort | Map single-end reads with hisat and output a sorted bam file |
| glue_se_star_bamsort | Map with STAR and output a sorted bam file |
| glue_star_genome_generate | Generate genome index for STAR |
| merge_featurecount_output | Merging read count tsv file from featureCounts |
| new_cmdopt | Create new cmdopt class object |
| param_general | Parameters for general use |
| param_genomeidx | Parameters for genome indexing commands |
| pipe | Pipe operator |
| pipeline_cuffdiff | pipeline for cufflinks |
| pipeline_cuffdiff_noRABT | pipeline for cufflinks |
| print.cmdopt | Print cmdopt class object |
| set_file_ext | Set file extensions |
| set_inf_class | Set inf class |
