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| Software | Description |
|---|---|
| abind | |
| cargo | |
| cowplot | |
| curl | |
| foreach | |
| gganimate | |
| GGally | |
| ggpubr | |
| ggrepel | |
| gifski | |
| gridSVG | |
| igraph | |
| jpeg | |
| leaps | |
| lme4 | |
| lubridate | |
| mirbase.db | |
| mixdist | |
| multcomp | |
| mvtnorm | |
| network | |
| pheatmap | |
| plotly | |
| plotROC | |
| plotrix | |
| quantmod | |
| RMySQL | |
| sna | |
| sqldf | |
| tidyr | |
| VGAM | |
| vioplot |
Additional R BioConductor Tools
| Software | Description |
|---|---|
| affy | |
| arrayQualityMetrics | |
| ballgown | Flexible, isoform-level differential expression analysis |
| BSgenome | Efficient genome searching |
| BSgenome.Hsapiens.UCSC.hg19 | |
| ChIPseeker | annotating ChIP-seq data analysis |
| cummeRbund | analyzing Cufflinks RNA-Seq output |
| DESeq2 | Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution |
| devtools | Collection of package development tools |
| DEXSeq | finding differential exon usage using RNA-seq exon counts between samples |
| GISPA | |
| GOstats | tools for interacting with GO and microarray data |
| GO.db | |
| JunctionSeq | |
| mirbase.db | |
| org.Sc.sgd.db | |
| org.Mm.eg.db | |
| rhdf5 | provides an interface between HDF5 and R |
| readr | |
| ReportingTools | |
| rhdf5 | |
| RIPSeeker | identify protein-associated transcripts from RIP-seq experiments |
| SISPA | |
| sleuth | analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto |
| ShortRead | sampling, iteration, and input of FASTQ files |
| topGO | |
| TxDb.Scerevisiae.UCSC.sacCer3.sgdGene | |
| TxDb.Hsapiens.UCSC.hg38.knownGene | |
| tximport | |
| WGCNA |
Additional Perl CPAN modules
...
| Software | Description | Path |
|---|---|---|
| bamtools | SAM/BAM file manipulation | /stor/system/opt/gitdir/bamtools/bin/bamtools |
| bcl2fastq | BCL file manipulation | /usr/bin/bcl2fastq |
| hisat | ||
| fastq_screen | ||
| samtools | SAM/BAM file manipulation | /usr/bin/samtools /usr/bin/samtools_0.1.18 /usr/bin/samtools-1.3 |
| picard | SAM/BAM file manipulation | /stor/system/opt/picard-tools-1.141 /stor/system/opt/picard-tools-2.5.0 |
bedtools | BED/GFF file manipulation | /usr/bin/bedtools-2.17.0 /usr/bin/bedtools-2.25.0 |
| sra toolkit | SRA file manipulation | /stor/system/opt/sratoolkit.2.7.0-ubuntu64 |
| stringtie | ||
| bwa | Alignment | /usr/bin/bwa |
RNA Sequencing Tools
| Software | Description | Path |
|---|---|---|
| augustus | ||
| busco | ||
| cufflinks | ||
| express | Expression quantification | /usr/bin/express |
| fastqc | ||
| featurecounts | Counting | /usr/bin/featureCounts |
| htseq | Counting | /stor/system/opt/HTSeq-0.6.1p1 |
| kallisto | Expression quantification | /usr/bin/kallisto |
| STAR | Alignment | /usr/bin/STAR /usr/bin/STARlong |
| tophat | ||
| MultiQC | Report Generation | /usr/bin/multiqc |
| RNA-SeQC | QC of RNA-seq alignments. To run this Java program: java -jar /stor/system/opt/rnaseqc/RNA-SeQC_v1.1.8.jar <other options> | /stor/system/opt/rnaseqc |
| hisat | Spliced alignment for mapping RNA-seq reads | /stor/system/opt/hisat-0.1.6-beta |
| hisat2 | Align NGS reads (both DNA and RNA) against a reference genome | /stor/system/opt/hisat2-2.0.5/ |
Specialized NGS Tools
| Software | Description | Path |
|---|---|---|
| BWA | ||
| MultiQC | Report Generation | /usr/bin/multiqc |
| eisen cluster | hierachical & k-means clustering | /usr/bin/cluster-eisen |
| imageJ | ||
| meme suite | motif analysis | /stor/system/opt/meme_4.11.2 |
| meme_chip | motif analysis suite for ChIP-seq | /stor/system/opt/software/meme-chip/4.11.2/ |
| art | next generation sequencing read simulator | /usr/bin/art_454 /usr/bin/art_illumina /usr/bin/art_SOLiD |
...