...
| 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 | k0.7.17-1ubuntu0.1-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 | 5.4.2-3ubuntu3.1 | shell with lots of features | y |
...
| 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 | Streamlined Plot Theme and Plot Annotations for 'ggplot2' | y | y | ||
| curl | A Modern and Flexible Web Client for R | y | y | ||
data.table | GNU R package “Extension of data.frame” | y | |||
dbi | GNU R package “R Database Interface” | ||||
| dbplyr | R Database Interface | y | y | ||
| dendextend | Extending 'dendrogram' Functionality in R | y | |||
dichromat | Color schemes for dichromats | y | |||
digest | GNU R package “Create Cryptographic Hash Digests of R | y | |||
| emmeans | Estimated Marginal Means, aka Least-Squares Means | y | y | ||
evaluate | GNU R package “Parsing and Evaluation Tools that Provide | y | |||
| fivethirtyeight | Data and Code Behind the Stories and Interactives at 'FiveThirtyEight' | y | y | ||
| forcats | Data and Code Behind the Stories and Interactives at 'FiveThirtyEight' | y | y | ||
| foreach | Provides Foreach Looping Construct | y | y | ||
futile.logger | GNU R package “A Logging Utility for R” | y | |||
futile.options | GNU R package “Futile options management” | y | |||
gdata | GNU R package “Various R Programming Tools for Data | y | |||
getopt | GNU R package “C-like getopt behavior.” | ||||
| gganimate | A Grammar of Animated Graphics | y | y | ||
| GGally | Extension to 'ggplot2' | y | y | ||
| ggExtra | Add Marginal Histograms to 'ggplot2', and More 'ggplot2' Enhancements | y | y | ||
ggplot2 | GNU R package “An Implementation of the Grammar of | y | |||
| ggpubr | 'ggplot2' Based Publication Ready Plots | y | y | ||
| ggrepel | Automatically Position Non-Overlapping Text Labels with 'ggplot2' | y | y | ||
| ggsci | Scientific Journal and Sci-Fi Themed Color Palettes for 'ggplot2' | y | y | ||
| ggsignif | Significance Brackets for 'ggplot2' | y | y | ||
| gifski | Highest Quality GIF Encoder | y | y | ||
| glmnet | Lasso and Elastic-Net Regularized Generalized Linear Models | y | y | ||
gplots | GNU R package “Various R Programming Tools for Plotting | y | |||
| gridSVG | Export 'grid' Graphics as SVG | y | y | ||
gtable | GNU R package “Arrange grobs in tables.” | y | |||
gtools | GNU R package “Various R Programming Tools” | y | |||
| haven | Import and Export 'SPSS', 'Stata' and 'SAS' Files | y | y | ||
| igraph | Network Analysis and Visualization | y | y | ||
| interactions | Comprehensive, User-Friendly Toolkit for Probing Interactions | y | y | ||
| jpeg | Read and write JPEG images | y | y | ||
labeling | GNU R package “Axis Labeling” | y | |||
lambda.r | GNU R package “Modeling Data with Functional Programming” | y | |||
lattice | GNU R package “Lattice Graphics” | y | |||
| latticeExtra | Extra Graphical Utilities Based on Lattice | y | y | ||
| leaps | GNU R package “regression subset selection” | y | 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 | y | ||
| locfit | Local Regression, Likelihood and Density Estimation | y | y | ||
| lubridate | Make Dealing with Dates a Little Easier | y | y | ||
matrix | GNU R package of classes for dense and sparse matrices | y | |||
matrixstats | R package “Methods that apply to rows and columns of a matrix” | y | |||
| mirbase.db | miRBase: the microRNA database | y | |||
| mixdist | Finite Mixture Distribution Models | y | y | ||
| modelr | Modelling Functions that Work with the Pipe | y | y | ||
| multcomp | Simultaneous Inference in General Parametric Models | y | y | ||
munsell | GNU R package “Munsell colour system” | y | |||
| mvtnorm | Multivariate Normal and t Distributions | y | y | ||
| network | Classes for Relational Data | y | y | ||
nlme | GNU R package for (non-)linear mixed effects models | y | |||
| nloptr | R Interface to NLopt | y | ontologyIndex | y | optparse |
| GNU R ontologyIndex | Functions for Reading Ontologies into R | y | y | ||
optparse | GNU R package “Command line option parser.” | ||||
permute | GNU R package “Functions for Generating Restricted | ||||
| pheatmap | Pretty Heatmaps | y | y | ||
| pbkrtest | Parametric Bootstrap and Kenward Roger Based Methods for Mixed Model Comparison | y | y | ||
| plotly | Create Interactive Web Graphics via 'plotly.js' | y | y | ||
| plotROC | Generate Useful ROC Curve Charts for Print and Interactive Use | y | y | ||
| plotrix | GNU R package “Various plotting functions” | y | y | ||
plyr | GNU R package “Tools for Splitting, Applying and Combining | y | |||
| polynom | A Collection of Functions to Implement a Class for Univariate Polynomial Manipulations | y | y | ||
proto | GNU R package “Prototype object-based programming” | y | y | ||
| quantmod | y | quantregQuantitative Financial Modelling Framework | y | y | |
| quantreg | Quantile Regression | y | y | ||
r.methodss3 | GNU R package “Utility function for defining S3 methods” | y | |||
rcolorbrewer | GNU R package providing suitable color palettes | y | |||
rcpp | GNU R package “Seamless R and C++ Integration” | y | |||
rcurl | GNU R package “General Network (HTTP/FTP/…) Client | y | |||
relimp | GNU R package “Relative Contribution of Effects in a | y | |||
reshape2 | GNU R package “Flexibly Reshape Data: A Reboot of the | y | y | ||
| reticulate | Interface to 'Python' | y | 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 | Database Interface and 'MySQL' Driver for R | y | y | ||
| ROCR | Visualizing the Performance of Scoring Classifiers | y | y | ||
rserve | GNU R Rserve tcp/ip server and sample clients | y | |||
| rstatix | Pipe-Friendly Framework for Basic Statistical Tests | y | y | ||
rsqlite | GNU R package “SQLite Interface for R” | y | |||
| rvest | Easily Harvest (Scrape) Web Pages | y | y | ||
scales | GNU R package “Scale Functions for Visualization” | y | |||
scatterplot3d | GNU R package “3D Scatter Plot” | y | y | ||
| servr | y | Seurat A Simple HTTP Server to Serve Static Files or Dynamic Documents | y | y | |
| Seurat | Tools for Single Cell Genomics | y | y | ||
| shape | Functions for Plotting Graphical Shapes, Colors | y | y | ||
| shiny | Web Application Framework for R | y | y | ||
| shinyjs | Easily Improve the User Experience of Your Shiny Apps in Seconds | y | y | ||
| sna | Tools for Social Network Analysis | y | y | ||
sp | GNU R package “Classes and Methods for Spatial Data” | ||||
| sqldf | y | statnet.commonsqldf | Manipulate R Data Frames Using SQL | y | y |
| statnet.common | Common R Scripts and Utilities Used by the Statnet Project Software | y | y | ||
stringr | GNU R package “Simple, Consistent Wrappers for Common | y | |||
tcltk2 | GNU R package “Tcl/Tk Additions” | y | y | ||
testthat | GNU R package “Testthat code. Tools to make testing fun | y | |||
| tibble | Simple Data Frames | y | y | ||
| tidyr | Tidy Messy Data | y | y | ||
| tidyverse | Easily Install and Load the 'Tidyverse' | y | y | ||
| transformr | Polygon and Path Transformations | y | y | ||
vegan | GNU R package “Community Ecology Package” | ||||
| VennDiagram | Generate High-Resolution Venn and Euler Plots | y | y | ||
| VGAM | Vector Generalized Linear and Additive Models | y | y | ||
| vioplot | Violin Plot | y | y | ||
| xfun | Miscellaneous Functions by 'Yihui Xie' | y | y | ||
xml | GNU R package “Tools for Parsing and Generating XML Within | y | y | ||
xtable | GNU R coerce data to LaTeX and HTML tables | y |
Additional R BioConductor Tools (cqbhiera/common.yaml) how to differentiate BioConductor tools
| Software | Description | in common.yaml | in library() |
|---|---|---|---|
| affy | Methods for Affymetrix Oligonucleotide Arrays | y | y |
| affyio | GNU R package “Tools for parsing Affymetrix data files” | y | |
| annotate | GNU R package “Annotation for microarrays” | y | |
annotationdbi | GNU R package “Annotation Database Interface” | y | |
| arrayQualityMetrics | Quality metrics report for microarray data sets | y | y |
| ballgown | Flexible, isoform-level differential expression analysis | y | y |
| biobase | GNU R package “Biobase: Base functions for Bioconductor” | y | |
biocgenerics | GNU R package “S4 generic functions for Bioconductor” | y | |
biocinstaller | GNU R package “Install/Update Bioconductor and CRAN | ||
biocparallel | GNU R package “Bioconductor facilities for parallel | y | |
biomart | GNU R Interface to BioMart databases (Ensembl, COSMIC, Wormbase and Gramene) | y | |
biostrings | GNU R package “String objects representing biological | y | |
| BSgenome | Efficient genome searching | y | y |
| BSgenome.Hsapiens.UCSC.hg19 | Full genome sequences for Homo sapiens (UCSC version hg19) | y | y |
| ChIPseeker | annotating ChIP-seq data analysis | y | y |
| cummeRbund | analyzing Cufflinks RNA-Seq output | y | 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 | y |
| devtools | Collection of package development tools | y | y |
| DEXSeq | finding differential exon usage using RNA-seq exon counts between samples | y | y |
| genfiltergenefilter | GNU R package “genefilter: methods for filtering genes | y | |
geneplotter | Graphics related functions for Bioconductor | y | |
genomeinfodb | GNU R package “Utilities for manipulating chromosome and | y | |
genomicalignments | GNU R package “Representation and manipulation of short | y | |
genomicranges | GNU R package “Representation and manipulation of genomic | y | |
| ggplot2movies | Movies Data | y | |
| GISPA | GISPA: Method for Gene Integrated Set Profile Analysis | y | y |
| GOstats | tools for interacting with GO and microarray data | y | y |
| GO.db | y | ||
hilbertvis | GNU R package to visualise long vector data | ||
| httpuv | HTTP and WebSocket Server Library | y | y |
iranges | GNU R package “Infrastructure for manipulating intervals | ||
| JunctionSeq | JunctionSeq: A Utility for Detection of Differential Exon and Splice-Junction Usage in RNA-Seq data | y | y |
limma | GNU R package “Linear Models for Microarray Data” | y | |
| mirbase.db | miRBase: the microRNA database | y | y |
multtest | GNU R package “Resampling-based multiple hypothesis | ||
| org.Hs.eg.db | Genome wide annotation for Human | y | y |
| org.Sc.sgd.dbsgd.db | Genome wide annotation for Yeast | y | y |
| org.Mm.eg.db | Genome wide annotation for Mouse | y | y |
| org.Rn.eg.db | Genome wide annotation for Rat | y | y |
preprocesscore | GNU R package “A collection of pre-processing functions” | y | |
| processx | Execute and Control System Processes | y | y |
| pkgload | y | ||
| qvalue | Bioconductor package “Q-value estimation for false discovery rate control” | y | |
| rhdf5 | provides an interface between HDF5 and R | y | y |
| readr | Read Rectangular Text Data | y | y |
| ReportingTools | Tools for making reports in various formats | y | y |
| RIPSeeker | identify protein-associated transcripts from RIP-seq experiments | y | y |
| roxygen2 | In-Line Documentation for R | y | y |
| rsamtools | GNU R package “Binary alignment (BAM), variant call (BCF), | y | |
s4vectors | GNU R package “S4 implementation of vectors and lists” SISPAof vectors and lists” | y | |
| SISPA | SISPA: Method for Sample Integrated Set Profile Analysis | y | y |
| sleuth | analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto | y | y |
| ShortRead | sampling, iteration, and input of FASTQ files | y | y |
| topGO | Enrichment Analysis for Gene Ontology | y | y |
| TxDb.Scerevisiae.UCSC.sacCer3.sgdGene | Annotation package for TxDb object(s) | y | y |
| TxDb.Hsapiens.UCSC.hg38.knownGene | Annotation package for TxDb object(s) | y | y |
| tximport | Import and summarize transcript-level estimates for transcript- and gene-level analysis | y | y |
| WGCNA | Weighted Correlation Network Analysis | y | y |
xvector | GNU R package “Representation and manpulation of external | y | |
| yardstick | Tidy Characterizations of Model Performance | y | y |
zlibbioc | GNU R package “An R packaged zlib-1.2.5″ | y |
Additional Perl CPAN modules (cqbprofile/manifest/perl.pp and cqb-maker)
...