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 |
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