...
| Software | Description | in common.yaml |
|---|---|---|
| abind | GNU R package “Combine multi-dimensional arrays” | y |
ade4 | GNU R package “Analysis of Ecological Data : Exploratory | |
| ape | GNU R package “Analyses of Phylogenetics and Evolution” | |
bitops | GNU R package implementing bitwise operations | |
| blogdown | y | |
| bookdown | y | |
catools | GNU R package “Tools: moving window statistics, GIF, | y |
| car | y | |
| cargo | y | |
cluster | GNU R package for cluster analysis by Rousseeuw et al | |
| colourpicker | y | |
| cowplot | y | |
| curl | y | |
data.table | GNU R package “Extension of data.frame” | |
dbi | GNU R package “R Database Interface” | |
| dbplyr | y | |
| dendextend | ||
dichromat | Color schemes for dichromats | |
digest | GNU R package “Create Cryptographic Hash Digests of R | |
| emmeans | y | |
evaluate | GNU R package “Parsing and Evaluation Tools that Provide | |
| fivethirtyeight | y | |
| forcats | y | |
| foreach | y | |
futile.logger | GNU R package “A Logging Utility for R” | |
futile.options | GNU R package “Futile options management” | |
gdata | GNU R package “Various R Programming Tools for Data | |
getopt | GNU R package “C-like getopt behavior.” | |
| gganimate | y | |
| GGally | y | |
| ggExtra | y | |
ggplot2 | GNU R package “An Implementation of the Grammar of | |
| ggpubr | y | |
| ggrepel | y | |
| ggsci | y | |
| ggsignif | y | |
| gifski | y | |
| glmnet | y | |
gplots | GNU R package “Various R Programming Tools for Plotting | |
| gridSVG | y | |
gtable | GNU R package “Arrange grobs in tables.” | |
gtools | GNU R package “Various R Programming Tools” | |
| haven | y | |
| igraph | y | |
| interactions | y | |
| jpeg | y | |
labeling | GNU R package “Axis Labeling” | |
lambda.r | GNU R package “Modeling Data with Functional Programming” | |
lattice | GNU R package “Lattice Graphics” | |
| latticeExtra | y | |
| leaps | GNU R package “regression subset selection” | y |
| libssl-dev | prereq? | y |
| libcairo2-dev | perreq? | y |
| libxt-dev | prereq? | y |
| libgmp10 | prereq? | y |
| libgmp-dev | prereq? | y |
| libmpfr6 | prereq? | y |
| libmpfr-dev | prereq? | y |
| lme4 | GNU R package for linear mixed effects model fitting | y |
| locfit | y | |
| lubridate | y | |
matrix | GNU R package of classes for dense and sparse matrices | |
matrixstats | R package “Methods that apply to rows and columns of a matrix” | |
| mirbase.db | ||
| mixdist | y | |
| modelr | y | |
| multcomp | y | |
munsell | GNU R package “Munsell colour system” | |
| mvtnorm | y | |
| network | y | |
nlme | GNU R package for (non-)linear mixed effects models | |
| nloptr | y | |
| ontologyIndex | y | |
optparse | GNU R package “Command line option parser.” | |
permute | GNU R package “Functions for Generating Restricted | |
| pheatmap | y | |
| pbkrtest | y | |
| plotly | y | |
| plotROC | y | |
| plotrix | GNU R package “Various plotting functions” | y |
plyr | GNU R package “Tools for Splitting, Applying and Combiningproto | |
| polynom | y | |
proto | GNU R package “Prototype object-based programming” | y |
| quantmod | y | |
| quantreg | y | |
r.methodss3 | GNU R package “Utility function for defining S3 methods” | |
rcolorbrewer | GNU R package providing suitable color palettes | |
rcpp | GNU R package “Seamless R and C++ Integration” | |
rcurl | GNU R package “General Network (HTTP/FTP/…) Client | |
relimp | GNU R package “Relative Contribution of Effects in a | y |
reshape2 | GNU R package “Flexibly Reshape Data: A Reboot of the | y |
| reticulate | y | |
rggobi | GNU R package for the GGobi data visualization system | y |
rgl | GNU R package for three-dimensional visualisation using OpenGL | |
rgtk2 | GNU R binding for Gtk2 | |
rmpi | GNU R package interfacing MPI libraries for distributed computing | y |
| RMySQL | y | |
| ROCR | y | |
rserve | GNU R Rserve tcp/ip server and sample clients | y |
| rstatix | y | |
rsqlite | GNU R package “SQLite Interface for R” | |
| rvest | y | |
scales | GNU R package “Scale Functions for Visualization” | |
scatterplot3d | GNU R package “3D Scatter Plot” | y |
| servr | y | |
| Seurat | y | |
| shape | y | |
| shiny | y | |
| shinyjs | y | |
| sna | y | |
sp | GNU R package “Classes and Methods for Spatial Data” | |
| sqldf | y | |
| statnet.common | y | |
stringr | GNU R package “Simple, Consistent Wrappers for Common | |
tcltk2 | GNU R package “Tcl/Tk Additions” | y |
testthat | GNU R package “Testthat code. Tools to make testing fun | |
| tibble | y | |
| tidyr | y | |
| tidyverse | y | |
| transformr | y | |
vegan | GNU R package “Community Ecology Package” | |
| VennDiagram | y | |
| VGAM | y | |
| vioplot | y | |
| xfun | y | |
xml | GNU R package “Tools for Parsing and Generating XML Within | y |
xtable | GNU R coerce data to LaTeX and HTML tables |
...
| Software | Description | |
|---|---|---|
| affy | y | |
| affyio | GNU R package “Tools for parsing Affymetrix data files” | |
| annotate | GNU R package “Annotation for microarrays” | |
annotationdbi | GNU R package “Annotation Database Interface” | |
| arrayQualityMetrics | y | |
| ballgown | Flexible, isoform-level differential expression analysis | y |
| biobase | GNU R package “Biobase: Base functions for Bioconductor” | |
biocgenerics | GNU R package “S4 generic functions for Bioconductor” | |
biocinstaller | GNU R package “Install/Update Bioconductor and CRAN | |
biocparallel | GNU R package “Bioconductor facilities for parallel | |
biomart | GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase and Gramene) | |
biostrings | GNU R package “String objects representing biological | |
| BSgenome | Efficient genome searching | y |
| BSgenome.Hsapiens.UCSC.hg19 | y | |
| ChIPseeker | annotating ChIP-seq data analysis | y |
| cummeRbund | analyzing Cufflinks RNA-Seq output | y |
| deseq | ||
| 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 | y |
| devtools | Collection of package development tools | y |
| DEXSeq | finding differential exon usage using RNA-seq exon counts between samples | y |
| genfilter | GNU R package “genefilter: methods for filtering genes | |
geneplotter | Graphics related functions for Bioconductor | |
genomeinfodb | GNU R package “Utilities for manipulating chromosome and | |
genomicalignments | GNU R package “Representation and manipulation of short | |
genomicranges | GNU R package “Representation and manipulation of genomic | |
| ggplot2movies | ||
| GISPA | y | |
| GOstats | tools for interacting with GO and microarray data | y |
| GO.db | y | |
hilbertvis | GNU R package to visualise long vector data | |
| httpuv | y | |
iranges | GNU R package “Infrastructure for manipulating intervals | |
| JunctionSeq | y | |
limma | GNU R package “Linear Models for Microarray Data” | |
| mirbase.db | y | |
multtest | GNU R package “Resampling-based multiple hypothesis | |
| org.Hs.eg.db | y | |
| org.Sc.sgd.db | y | |
| org.Mm.eg.db | y | |
| org.Rn.eg.db | y | |
preprocesscore | GNU R package “A collection of pre-processing functions” | |
| processx | y | |
| pkgload | y | |
| qvalue | Bioconductor package “Q-value estimation for false discovery rate control” | |
| rhdf5 | provides an interface between HDF5 and R | y |
| readr | y | |
| ReportingTools | y | |
| RIPSeeker | identify protein-associated transcripts from RIP-seq experiments | y |
| roxygen2 | y | |
| rsamtools | GNU R package “Binary alignment (BAM), variant call (BCF), | |
s4vectors | GNU R package “S4 implementation of vectors and lists” | |
| SISPA | y | |
| sleuth | analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto | y |
| ShortRead | sampling, iteration, and input of FASTQ files | y |
| topGO | y | |
| TxDb.Scerevisiae.UCSC.sacCer3.sgdGene | y | |
| TxDb.Hsapiens.UCSC.hg38.knownGene | y | |
| tximport | y | |
| WGCNA | y | |
xvector | GNU R package “Representation and manpulation of external | |
| yardstick | y | |
zlibbioc | GNU R package “An R packaged zlib-1.2.5″ |
Additional Perl CPAN modules (cqbprofile/manifest/perl.pp and cqb-maker)
| Software | Description | CGI | DBI | Graph | LWPin perl.pp or cqb-maker? |
|---|---|---|---|---|---|
| Bit::Vector | y | ||||
| CGI | y | ||||
| DBI | y | ||||
| DBD::SQLite | y | ||||
| File::Which | y | ||||
| forks | y | ||||
| forks::shared | y | ||||
| Graph | y | ||||
| IO::All | y | ||||
| IO:Prompt | y | ||||
| LWP | y | ||||
| Math::Cephes | y | ||||
| Module::Build | y | ||||
| Net::HTTP | y | ||||
| Perl::Unsafe::Signals | y | ||||
| Statistics::Descriptive | y | ||||
| Switch | y | ||||
| Test::Class | y | ||||
| Test::More | y | ||||
| Test::Exception | y | ||||
| Test::Harness | y | ||||
| XML::Simple | y |
Next Generation Sequencing (NGS) Tools (cqbprofile/manifest/next_gen_sequencing_client.pp)
| Software | Description | Path | in next_gen_sequencing_client.pp |
|---|---|---|---|
| bamtools | SAM/BAM file manipulation | /stor/system/opt/gitdir/bamtools/bin/bamtools | y |
| bcl2fastq | BCL file manipulation | /usr/bin/bcl2fastq | y |
| deeptools | y | ||
| enabrowsertools | y | ||
| hisat | y | ||
| fastq_screen | |||
| guppy | y | ||
| 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 | y |
bedtools | BED/GFF file manipulation | /usr/bin/bedtools-2.17.0 /usr/bin/bedtools-2.25.0 | y |
| samtools | y | ||
| scalangs | y | ||
| sra toolkit | SRA file manipulation | /stor/system/opt/sratoolkit.2.7.0-ubuntu64 | y |
| stringtie | y | ||
| bwa | Alignment | /usr/bin/bwa |
RNA Sequencing Tools (cqbprofile/manifest/rna_sequencing_client.pp)
| Software | Description | Path | in rna_sequencing_client.pp |
|---|---|---|---|
| augustus | y | ||
| busco | y | ||
| cellranger | y | ||
| cufflinks | y | ||
| express | Expression quantification | /usr/bin/express | y |
| fastqc | y | ||
| featurecounts | Counting | /usr/bin/featureCounts | y |
| htseq | Counting | /stor/system/opt/HTSeq-0.6.1p1 | y |
| kallisto | Expression quantification | /usr/bin/kallisto | y |
| STAR | Alignment | /usr/bin/STAR /usr/bin/STARlong | y |
| tophat | y | ||
| MultiQC | Report Generation | /usr/bin/multiqc | y |
| 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 | y |
| salmon | y | ||
| 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 ((specialized_sequencing_client.pp)
| Software | Description | Path | in specialized_sequencing_client.pp |
|---|
...
| Software | |||
|---|---|---|---|
| BWA | Descriptiony | Path||
| bwa_mem2 | BWAy | ||
| MultiQC | Report Generation | /usr/bin/multiqc | |
| eisen cluster | hierachical & k-means clustering | /usr/bin/cluster-eisen | y |
| imageJ | y | ||
| 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/ | y |
| art | next generation sequencing read simulator | /usr/bin/art_454 /usr/bin/art_illumina /usr/bin/art_SOLiD | y |
Variant Analysis Tools (variant_analysis_client.pp)
NB: These tools are only available on select PODs. At this time of this writing, it included the GSAF and Iyer PODs.
| Software | Description | Path | in variant_analysis_client.pp |
|---|---|---|---|
| annovar | Annotation of variants | /stor/system/opt/annovar/ | y |
| gatk | Human/higher-vertabrate variant detection toolkit | /stor/system/opt/gatk-3.6/ | y |
| MuTect | Somatic Mutations | /stor/system/opt/gatk-3.6/ /stor/system/opt/mutect/ | y |
| plink | GWAS tools | /usr/bin/plink | y |
| snpeff | Genetic variant annotation and effect prediction | /stor/system/opt/snpEff | y |
Evolutionary Analysis Tools (evolution_sequencing_client.pp)
Note: These tools are only available on select PODs. At this time of this writing, it included the GSAF POD.
| Software | Description | Path | in evolution_sequencing_client.pp? |
|---|---|---|---|
| mauve | y |
Genome/Transcriptome Assembly Tools genome_client.pp
Note: These tools are only available on select PODs. At this time of this writing, it included the GSAF and Educational PODs.
| Software | Description | Path | in genome_client.pp |
|---|---|---|---|
| consed | contig assembly tools | /usr/local/genome/consed/ | y |
| phrap | contig assembly tools | /usr/local/genome/bin/ | y |
| phred | contig assembly tools | /usr/local/genome/bin/ | y |
| glimmer | micobial gene annotations | /usr/bin/glimmer2 /usr/bin/build-icm /usr/bin/extract /usr/bin/long-orfs | y |
Web-based application software (add Python and R versions)
...