...
| Software | Version | Description | in cqb-biolinux? |
|---|---|---|---|
2.0.2-3 | de novo, parallel, sequence assembler for short reads | y | |
bamtools | 2.4.1+dfsg-2 | toolkit for manipulating BAM (genome alignment) files | y |
bedtools | 2.26.0+dfsg-5 | suite of utilities for comparing genomic features | y |
| bioperl | 1.7.2-2 | Perl tools for computational molecular biology | y |
bioperl-run | 1.7.1-3 | BioPerl wrappers: scripts | y |
| blast2 | 1:2.6.0-1 | Basic Local Alignment Search Tool | y |
| bowtie | 1.2.2+dfsg-2 | Ultrafast memory-efficient short read aligner | y |
| bowtie2 | 2.3.4.1-1 | Ultrafast memory-efficient short read aligner | n |
| bwa | 0.7.17-1ubuntu0.1 | Burrows-Wheeler Aligner | n |
| cd-hit | 4.6.8-1 | a suite of programs designed to quickly group sequences | y |
clustalw | 2.1+lgpl-5 | No description | y |
clustalx | 2.1+lgpl-6 | No description | y |
cufflinks | 2.2.1+dfsg.1-2 | Transcript assembly, differential expression and regulation for RNA-Seq | n |
ea-utils | 1.1.2+dfsg-4build1 | command-line tools for processing biological sequencing data | y |
emboss | 6.6.0+dfsg-6build1 | european molecular biology open software suite | n |
emboss-lib | 6.6.0+dfsg-6build1 | EMBOSS Libraries | y |
fastdnaml | 1.2.2-12 | Tool for construction of phylogenetic trees of DNA sequences | y |
fastqc | 0.11.5+dfsg-6 | A quality control application for high throughput sequence data | n |
fastx-toolkit | 0.0.14-5 | FASTQ/A short nucleotide reads pre-processing tools | y |
hmmer | 3.1b2+dfsg-5ubuntu1 | profile hidden Markov models for protein sequence analysis | n |
jaligner | 1.0+dfsg-4 | Smith-Waterman algorithm with Gotoh’s improvement | y |
jellyfish | 2.2.8-3build1 | count k-mers in DNA sequences | y |
khmer | 2.1.2+dfsg-3 | kk0.7.17-1ubuntu0.1-mer counting, filtering and graph traversal | y |
libbiojava-java | 1:1.7.1-7 | Java API to biological data and applications (default version) | y |
libbiojava-java-demos | 1:1.7.1-7 | Example programs for BioJava | y |
macs | 2.1.1.20160309-2 | Model-based Analysis of ChIP-Seq on short reads sequencers | y |
mafft | 7.310-1 | Multiple alignment program for amino acid or nucleotide sequences | y |
maq | 0.7.1-7 | maps short fixed-length polymorphic DNA sequence reads to reference sequences | y |
| med-bio | 3.0.1ubuntu1 | Debian Med bioinformatics packages | y |
| med-cloud | 3.0.1ubuntu1 | Debian Med bioinformatics applications usable in cloud computing | y |
microbiomeutil | 20101212+dfsg1-1build1 | Microbiome Analysis Utilities | y |
mothur | 1.39.5-2build1 | sequence analysis suite for research on microbiota | y |
mothur-mpi | 1.39.5-2build1 | mpi-enabled binary for mothur | y |
mrbayes-mpi | 3.2.6+dfsg-2 | Bayesian Inference of Phylogeny – mpi version | y |
mummer | 3.23+dfsg-3 | Efficient sequence alignment of full genomes | y |
muscle | 1:3.8.31+dfsg-3 | Multiple alignment program of protein sequences | y |
ncbi-blast+ | 2.6.0-1 | next generation suite of BLAST sequence search tools | n |
ncbi-blast+-legacy | 2.6.0-1 | NCBI Blast legacy call script | n |
ncbi-seg | 0.0.20000620-4 | tool to mask segments of low compositional complexity in amino acid sequences | y |
ncbi-tools-bin | 6.1.20170106-2 | NCBI libraries for biology applications (text-based utilities) | y |
ncbi-tools-x11 | 6.1.20170106-2 | NCBI libraries for biology applications (X-based utilities) | y |
paml | 4.9g+dfsg-3 | Phylogenetic Analysis by Maximum Likelihood (PAML) | y |
parafly | 0.0.2013.01.21-3build1 | parallel command processing using OpenMP | y |
phylip | 1:3.696+dfsg-5 | No description | y |
phyml | 3:3.3.20170530+dfsg-2 | Phylogenetic estimation using Maximum Likelihood | y |
picard-tools | 2.8.1+dfsg-3 | Command line tools to manipulate SAM and BAM files | y |
primer3 | 2.4.0-1ubuntu2 | Tool to design flanking oligo nucleotides for DNA amplification | y |
pymol | 1.8.4.0+dfsg-1build1 | Molecular Graphics System | y |
qiime | 3:3.3.20170530+dfsg-2 (1.8.0+dfsg-4ubuntu1)? | Quantitative Insights Into Microbial Ecology | y |
rasmol | 2.7.5.2-2 | Visualize biological macromolecules | y |
raxml | 8.2.11+dfsg-1 | Randomized Axelerated Maximum Likelihood of phylogenetic trees | y |
readseq | 1-12 | Conversion between sequence formats | y |
rsem | 1.2.31+dfsg-1 | RNA-Seq by Expectation-Maximization | y |
samtools | 1.7-1 | processing sequence alignments in SAM and BAM formats | n |
sift | 4.0.3b-6 | predicts if a substitution in a protein has a phenotypic effect | y |
sortmerna | 2.1-2 | tool for filtering, mapping and OTU-picking NGS reads | y |
stacks | 2.0Beta8c+dfsg-1 | pipeline for building loci from short-read sequences | y |
sumatra | 1.0.31-1 | fast and exact comparison and clustering of sequences | y |
swarm | 2.2.2+dfsg-1 | robust and fast clustering method for amplicon-based studies | y |
t-coffee | 2.2.2+dfsg-1 (11.00.8cbe486-6) | Multiple Sequence Alignment | n |
tophat | 2.1.1+dfsg1-1 | fast splice junction mapper for RNA-Seq reads | n |
transdecoder | 5.0.1-1 | find coding regions within transcripts | y |
trinityrnaseq | 2.5.1+dfsg-2 | RNA-Seq De novo Assembly | y |
trnascan-se | 1.3.1-1 | search for tRNA genes in genomic sequences | y |
velvet | 1.2.10+dfsg1-3build1 | Nucleic acid sequence assembler for very short reads | y |
velvet-example | 1.2.10+dfsg1-3build1 | Example data for the Velvet sequence assembler | y |
velvet-long | 1.2.10+dfsg1-3build1 | Nucleic acid sequence assembler for very short reads, long version | y |
velvetoptimiser | 2.2.6-1 | Automatically optimise Velvet do novo assembly parameters | y |
vsearch | 2.7.1-1 | tool for processing metagenomic sequences | y |
| zsh | y |
...
| 5.4.2-3ubuntu3.1 | shell with lots of features | y |
Standard Third-Party Software (versions?)
| Software | Description | Version |
|---|---|---|
| R, Rscript | R command-line shell and script execution programs. | 3.4.4, 3.5.3, 3.6.1 |
| Matlab | MathWorks Matlab Software. See How do I use MATLAB on the POD? |
...
Additional Python Tools (cqb-devel_tools/manifests/python.pp) find version with pip (pip3 freeze | grep xopen)
| Software | Python2 Version | Python3 Version | Description | in devel_tools |
|---|---|---|---|---|
| all-dev | y | |||
| blaze | 0.10.1 | 0.10.1 | An interface to query data on different storage systems | y |
| cutadapt | 1.18 | 1.18 | Finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads | y |
| dendropy | phylogenetic computing | y | ||
| freetype-dev (libfreetype6-dev) | y | |||
| leukgen-disambiguate | 1.0.1 | 1.0.1 | y | |
| MACS2 | 2.1.2 | Model Based Analysis for ChIP-Seq data | y | |
| maplot | y | |||
| matplotlib | python 2D plotting library | y | ||
| networkx | 1.0.2 | 1.0.2 | y | |
| matplotlib | 2.1.1 | 3.2.1 | python 2D plotting library | y |
| networkx | 2.2 | 2.0 | Creation, manipulation, and study of the structure, dynamics, and functions of complex networks. | y |
| nimfa | 1.3.4 | 1.3.4 | Nonnegative matrix factorization | y |
| numpy | 1.13.3 | 1.13.3 | scientific computing with Python | y |
| pandas | 0.22.0 | 0.22.0 | Python Data Analysis Library | y |
| patsy | 0.4.1+dev | 0.2.1 | y | |
| pip | Python installation program (to install python modules) | y | ||
| plotly | 4.0.0 | 4.0.0 | y | |
| pysam | 0.8.4 | 0.8.4 | y | |
| pyvttbl | 0.5.2.2 | 0.5.2.2 | y | |
| reportlab (->biopython?) | 3.4.0 (->1.70) | 3.5.12 (->1.73) | y | |
| rpy2 | 2.8.6 | 2.9.2 | Python interface to R | y |
| seaborn | 0.8.1 | 0.8.1 | y | |
| scipy | 0.19.1 | 0.19.1 | Collection of Python software for mathematics, science, and engineering. | y |
| sklearn | Machine Learning in Python | y | ||
| skimage | Image processing in Python | ystatsmodels | ||
| statsmodels | 0.8.0 | 0.8.0 | Estimation of statistical models | y |
Additional R Tools (cqbhiera/common.yaml dont appear to have versions)
| Software | Description | in common.yaml | listed in library() |
|---|---|---|---|
| abind | GNU R package “Combine multi-dimensional arrays” | y | y |
ade4 | GNU R package “Analysis of Ecological Data : Exploratory | y | |
| ape | GNU R package “Analyses of Phylogenetics and Evolution” | y | |
bitops | GNU R package implementing bitwise operations | y | |
| blogdown | Create Blogs and Websites with R Markdown | y | y |
| bookdown | Authoring Books and Technical Documents with R Markdown | y | y |
catools | GNU R package “Tools: moving window statistics, GIF, | y | y |
| car | Companion to Applied Regression | y | y |
| cargo | y | n | |
cluster | GNU R package for cluster analysis by Rousseeuw et al | y | |
| colourpicker | A Colour Picker Tool for Shiny and for Selecting Colours in Plots | y | 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 Combining | ||
| 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 |
Additional R BioConductor Tools (cqbhiera/common.yaml) how to differentiate BioConductor tools
| 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″ |
...