Man pages for e-myers/rnaseq
Process, Analyze and Visualize RNA-seq Data
| bam_strand_split | Split BAM with paired-end data into forward-strand and... |
| bamToBed | Convert BAM files to bed format |
| bedgraph_flip | Convert bedgraph values between positive and negative |
| bedgraphToBigWig | Bedgraph files to bigwig format |
| computeMatrix | Read density per region |
| count_alignments | Get alignment counts from BAM files |
| count_features | Read in raw counts for genomic features |
| count_reads | Get read counts from fastqs |
| counts_to_tpm | Get transcripts per million |
| count_summaries | Get read counts from featureCounts summary files |
| cutadapt_run | Trim reads in fastq files |
| dir_check | Check directory existence |
| exprHeatmap | Expression heatmaps |
| exprLFC | Log2 fold change heatmap |
| exprMean | Mean expression heatmaps |
| featureCounts_run | Read counts from BAM or SAM files |
| file_checks | Check file existence / extension |
| genomeCoverageBed | BAM or bed files to bedgraph with histogram of coverage... |
| genomic_ranges_reduce | Reduce genomic ranges to set of non-overlapping ranges |
| get_expr | Get counts or TPM matrix |
| hello | Hello, World! |
| plotHeatmap | Read density per region - heatmap |
| sam_filter | Filter SAM file |
| sam_to_bam | SAM files filtered and converted to BAM format |
| STAR_run | Map reads to genome |
| transcript_to_gene_fix | Replace transcript ids with gene ids in GTF file |
| transcript_to_gene_map | Create file associating transcript ids with gene ids |
