...
| Software | Description | Access |
|---|---|---|
| JupyterHub Server | Python Notebook Server | Available on all compute servers https://<server_name>.ccbb.utexas.edu |
| R Studio Server | R Studio Web Interface |
Standard OS Software
(
...
to find in repo
...
: frep -r pattern .| grep -v /spec/)
| Software | Description |
|---|---|
| build-essential | gcc, g++, make, cmake, patch, autoconf, automake, m4, bison, libtool |
| emacs, vi, vim, ed | text editors |
| postfix | mail programs |
| perl | perl interpretor |
| python 2 | python version 2 interpretor |
| python 3 | python version 3 interpretor |
| ruby | ruby programming language |
| samba | Windows SMB/CIFS file and printer sharing protocol and applications |
| screen, tmux | Text window managers (multiplexer) |
| ssh | Secure Shell (remote access) |
| sudo | Root access for POD delegates only |
| tar | File archiving utility |
| wget, curl | Remote file/url transfer utilities |
| gzip, zip, unzip | File compression and archiving tools. |
| scons | Software build tool |
| swig | Software development tool |
| sqlite3 | SQL Lite databases |
| git | Version control utilities |
Standard BioLinux Packages
(
...
find using: dpkg -l bioperl)
...
R modules in repo common.yaml
| 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 | |
| bwa | 0.7.17-1ubuntu0.1 | Burrows-Wheeler Aligner | |
| 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 | |
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 | |
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 | |
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 | |
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 packagesy | |
| 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 | |
ncbi-blast+-legacy | 2.6.0-1 | NCBI Blast legacy call script | |
ncbi-seg | 0.0.20000620-4 | tool to mask segments of low compositional complexity in amino acid sequences | y |
ncbincbi-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 | |
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 | |
tophat | 2.1.1+dfsg1-1 | fast splice junction mapper for RNA-Seq reads | |
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 featuresy |
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? | |
| docker | OS-level virtualization to deliver software in packages called containers |
Additional Python Tools
(in repo under 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 | |||
| blazeblaze | 0.10.1 | 0.10.1 | An interface to query data on different storage systemsy | |
| 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) | This package contains all of the supplementary files you need to develop your own programs using the FreeType 2 library. | y | ||
| leukgen-disambiguate | 1.0.1 | 1.0.1 | Disambiguate reads mapping to multiple genomes. This is a frozen release with some bug fixes of the original AstraZeneca-NGS/disambiguate v1.0. | y |
| MACS2 | 2.1.2 | Model Based Analysis for ChIP-Seq data | y | |
| maplot | 1.0.2 | 1.0.2 | Python package for creating interactive MA-plotsy | |
| 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 Libraryy | |
| patsy | 0.4.1+dev | 0.2.1 | Patsy is a Python library for describing statistical models (especially linear models, or models that have a linear component) and building design matrices. Patsy brings the convenience of R “formulas” to Python. | y |
| pip | Python installation program (to install python modules)y | |||
| plotly | 4.0.0 | 4.0.0 | An open-source, interactive data visualization library for Python y | |
| pysam | 0.8.4 | 0.8.4 | a python module for reading, manipulating and writing genomic data sets | y |
| pyvttbl | 0.5.2.2 | 0.5.2.2 | Multidimensional pivot tables, data processing, statistical computationy | |
| reportlab (->biopython?) | 3.4.0 (->1.70) | 3.5.12 (->1.73) | The ReportLab Toolkit. An Open Source Python library for generating PDFs and graphics. (→ Freely available tools for computational molecular biology) | y |
| rpy2 | 2.8.6 | 2.9.2 | Python interface to Ry | |
| seaborn | 0.8.1 | 0.8.1 | statistical data visualizationy | |
| 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 | y | ||
| statsmodels | 0.8.0 | 0.8.0 | Estimation of statistical models | y |
| pytorch/torch | 1.7.0 | 1.7.0 | Optimized tensor library for deep learning | |
torchvision | 0.8.1 | 0.8.1 | popular datasets, model architectures, and common image transformations for computer vision |
Additional R Tools
(in repo cqbhiera/common.yaml
...
)
| 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 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 | |||
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 Interfacey | y | ||
| dendextend | Extending 'dendrogram' Functionality in Ry | |||
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 | ||
| ggpubrggpubr | 'ggplot2' Based Publication Ready Plotsy | 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 | |
| gt | Build display tables from tabular data with an easy-to-use set of functions | 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 Visualizationy | 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 | ||
| lme4lme4 | 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 Distributionsy | 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 | y | |
| 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 | Quantitative quantmod | Quantitative 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 Ry | 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 | 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 | ||
| showtext | Making it easy to use various types of fonts in R graphs | |||
| showtextdb | Providing font files that can be used by the 'showtext' package | |||
| Signac | A framework for the analysis of single-cell chromatin data | |||
| ysna | sna | Tools for Social Network Analysis | y | y |
sp | GNU R package “Classes and Methods for Spatial Data” | |||
| sqldf | 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 | |||
| sysfonts | Loading system fonts and Google Fonts into R | |||
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 | yy | ||
| tidyverse | Easily Install and Load the 'Tidyverse' | y | y | |
| transformr | Polygon and Path Transformationsy | 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
(in repo cqbhiera/common.yaml)
...
| 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 searchingy | 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 |
| EnhancedVolcano | Publication-ready volcano plots with enhanced colouring and labeling | y | |
| genefilter | 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 Datay | ||
| 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 Libraryy | 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 databasey | y | |
multtest | GNU R package “Resampling-based multiple hypothesis | ||
| org.Hs.eg.db | Genome wide annotation for Human | y | y |
| org.Sc.sgd.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 experimentsy | y | |
| roxygen2 | In-Line Documentation for Ry | y | |
| rsamtools | GNU R package “Binary alignment (BAM), variant call (BCF), y | ||
s4vectors | GNU R package “S4 implementation of 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 Analysisy | y | |
xvector | GNU R package “Representation and manpulation of external y | ||
| yardstick | Tidy Characterizations of Model Performancey | y | |
zlibbioc | GNU R package “An R packaged zlib-1.2.5″ y |
Additional Perl CPAN modules
(in repo cqbprofile/manifest/perl.pp and cqb-maker)
| Software | Description | in perl.pp or cqb-maker?|
|---|---|---|
| Bit::Vector | y | |
| CGI | y | |
| DBI | y | |
| DBD::SQLitey | ||
| File::Whichy | ||
| forks | y | |
| forks::shared | y | |
| Graph | y | |
| IO::Ally | ||
| IO:Prompty | ||
| LWP | y | |
| Math::Cephesy | ||
| Module::Build | y | |
| Net::HTTPy | ||
| Perl::Unsafe::Signalsy | ||
| Statistics::Descriptive | y | |
| Switch | y||
| Test::Classy | ||
| Test::Morey | ||
| Test::Exception | y | |
| Test::Harness | y | |
| XML::Simple | y |
Next Generation Sequencing (NGS) Tools
(in repo 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/bamtoolsy | |
| bcl2fastq | BCL file manipulation | /usr/bin/bcl2fastqy | |
| deeptools | y | ||
| enabrowsertoolsy | |||
| hisat | y | ||
| fastq_screen | |||
| guppyy | |||
| 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-2.5.0y | |
bedtools | BED/GFF file manipulation | /usr/bin/bedtools-2.17.0 /usr/bin/bedtools-2.25.0 | y |
| samtoolsy | |||
| scalangsy | |||
| sra toolkit | SRA file manipulation | /stor/system/opt/sratoolkit.2.7.0-ubuntu64y | |
| stringtie | y | ||
| bwa | Alignment | /usr/bin/bwa |
RNA Sequencing Tools
(in repo cqbprofile/manifest/rna_sequencing_client.pp)
| Software | Description | Path | in rna_sequencing_client.pp |
|---|---|---|---|
| augustus | program to find genes and their structures in one or more genomes | y | |
| busco | y | ||
| cellranger | y | ||
| cufflinksy | |||
| express | Expression quantification | /usr/bin/expressy | |
| fastqc | y | ||
| featurecounts | Counting | /usr/bin/featureCountsy | |
| htseq | Counting | /stor/system/opt/HTSeq-0.6.1p1 | y |
| kallisto | Expression quantification | /usr/bin/kallistoy | |
| STAR | Alignment | /usr/bin/STAR /usr/bin/STARlongy | |
| tophat | y | ||
| MultiQC | Report Generation | /usr/bin/multiqcy | |
| 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/rnaseqcy | |
| salmony | |||
| 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/ | |
| gossamer | bioinformatics suite including goss, gossple, xenome, and electus | /usr/local/bin/goss /usr/local/bin/gossple /usr/local/bin/xenome /usr/local/bin/electus | y |
Specialized NGS Tools
(in repo specialized_sequencing_client.pp)
| Software | Description | Path | in specialized_sequencing_client.pp |
|---|---|---|---|
| BWA | y | ||
| bwa_mem2 | y | ||
| MultiQC | Report Generation | /usr/bin/multiqc | |
| eisen cluster | hierachical & k-means clustering | /usr/bin/cluster-eisen | y |
| imageJy | |||
| 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 | Pathin 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 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 |
| ISEScan | identification of insertion sequence elements in genomes | /usr/lib/libssw.so | y |
| FragGeneScan | requirement of ISEScan | /usr/bin/FragGeneScan1.30y |
Molecular Structures Client
| Software | Description | Pathin molecular_structures_client.pp |
|---|---|---|
| gromacs | package to perform molecular dynamics | |
| mgltools | software for visualization and analysis of molecular structures | |
| nwchem | computes properties of molecular and periodic systems |
...
| Software | Description | Location | Path | ||
|---|---|---|---|---|---|
| bam2fastq | Iyer POD | /stor/system/opt/bam2fastq-1.1.0/ | |||
| basespace | GSAF POD | ||||
| canu | Chen POD | ||||
| crossstitch | Ochman POD | docker | Marcotte POD | ||
| falcon | Chen POD | ||||
| irodsfs | Not yet fully supported | gsafcbig01 | /mnt/corral | ||
| maker | Ochman POD | ||||
| R bitops | |||||
| R caTools | Iyer POD | ||||
| R snow | Iyer POD | ||||
| R Snowfall | |||||
| R phantompeakqualtools | Iyer POD | ||||
| R NCIS | Iyer POD | ||||
| volalign | Marcotte POD |
...