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http://broadinstitute.github.io/picard/
Java toolset for working with next generation sequencing data in the BAM format.
Proper citation: Picard (RRID:SCR_006525) Copy
Software package for statistical analysis and presentation of graphics. Statistical software for data science.
Proper citation: Stata (RRID:SCR_012763) Copy
http://tcoffee.crg.cat/apps/tcoffee/do:regular
A multiple sequence alignment server which can align Protein, DNA and RNA sequences.
Proper citation: T-Coffee (RRID:SCR_011818) Copy
Efficient protein multiple sequence alignment program, which has demonstrated a statistically significant improvement in accuracy compared to several leading alignment tools.
Proper citation: ProbCons (RRID:SCR_011813) Copy
http://genevenn.sourceforge.net/
A web application creating Venn diagrams from two or three gene lists.
Proper citation: GeneVenn (RRID:SCR_012117) Copy
http://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=tblastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
Tool to search translated nucleotide databases using a protein query.
Proper citation: TBLASTN (RRID:SCR_011822) Copy
http://nhjy.hzau.edu.cn/kech/swxxx/jakj/dianzi/Bioinf6/GeneFinding/GeneFinding2.htm
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 10,2020. Data analysis service for Hidden Markov Model (HMM)-based gene structure prediction (multiple genes, both chains).
Proper citation: FGENESH (RRID:SCR_011928) Copy
http://gpcr.biocomp.unibo.it/bacello/
A predictor for the subcellular localization of proteins in eukaryotes that is based on a decision tree of several support vector machines (SVMs). It classifies up to four localizations for Fungi and Metazoan proteins and five localizations for Plant ones. BaCelLo's predictions are balanced among different classes and all the localizations are considered as equiprobable.
Proper citation: BaCelLo (RRID:SCR_011965) Copy
http://support.illumina.com/sequencing/sequencing_software/casava.html
Software package that creates genomic builds, calls SNPs, detects indels, and counts reads from data generated from one or more sequencing runs. In addition, CASAVA automatically generates a range of statistics, such as mean depth and percentage chromosome coverage, to enable comparison with previous builds or other samples. CASAVA analyzes sequencing reads in three stages: * FASTQ file generation and demultiplexing * Alignment to a reference genome * Variant detection and counting
Proper citation: CASAVA (RRID:SCR_001802) Copy
https://www.schrodinger.com/ligprep
Software tool to correct and optimize the ligands by generating different protonation states, stereochemistry, tautomers, and ring conformations. Used to generate accurate, energy minimized 3D molecular structures.
Proper citation: Ligprep (RRID:SCR_016746) Copy
https://www.schrodinger.com/epik
Software program for pKa prediction and protonation state generation for drug like molecules.
Proper citation: Epik (RRID:SCR_016745) Copy
Software Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks.
Proper citation: NetworkX (RRID:SCR_016864) Copy
https://github.com/cancerit/BRASS
Software tool for analysis of one or more related BAM files of paired end sequencing to determine potential rearrangement breakpoints. Identifies breaks and attempts to assemble rearrangements.
Proper citation: BRASS (RRID:SCR_017091) Copy
https://github.com/aldenleung/OMTools
Software package for optical mapping data processing, analysis and visualization. Used to handle and explore large scale optical mapping profiles.
Proper citation: OMTools (RRID:SCR_017143) Copy
Software platform to explore, analyze and visualize data. SAS 9.4 is part of SAS Platform. Standardized data governance and management from statistical software company SAS.
Proper citation: Statistical Analysis System (RRID:SCR_008567) Copy
A Python-based environment of open-source software for mathematics, science, and engineering. The core packages of SciPy include: NumPy, a base N-dimensional array package; SciPy Library, a fundamental library for scientific computing; and IPython, an enhanced interactive console.
Proper citation: SciPy (RRID:SCR_008058) Copy
https://www.indicalab.com/halo/
Software image analysis platform for quantitative tissue analysis in digital pathology by Indica Labs. Used for high-throughput, quantitative tissue analysis in oncology, neuroscience, metabolism, toxicology.
Proper citation: HALO (RRID:SCR_018350) Copy
https://github.com/Tarskin/LaCyTools
Software high throughput data extraction package for LC-MS data.Targeted Liquid Chromatography-Mass Spectrometry data processing package for relative quantitation of glycopeptides.
Proper citation: LaCyTools (RRID:SCR_024525) Copy
https://CRAN.R-project.org/package=GOplot
Software R package for visually combining expression data with functional analysis.
Proper citation: GOplot (RRID:SCR_024419) Copy
https://CRAN.R-project.org/package=geepack
Software R package implements generalized estimating equations for parameters in mean, scale, and correlation structures, through mean link, scale link, and correlation link. Can handle clustered categorical responses. Used for fitting marginal generalized linear models to clustered data.
Proper citation: geepack (RRID:SCR_024510) Copy
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