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https://github.com/pachterlab/kb_python
Software Python package that wraps kallisto and bustools single-cell RNA-seq workflow. Used for single-cell RNA-seq pre-processing. Simplifies downloading and running of kallisto and bustools programs. Consists of kb ref and kb count commands. kb ref builds or downloads species specific index for pseudo alignment of reads and must be run prior to kb count and it runs kallisto index. kb count runs kallisto and bustools programs and is used for pre-processing of data from variety of single-cell RNA-seq technologies, and for number of different workflows (e.g. production of gene count matrices, RNA velocity analyses, etc.).
Proper citation: kb_python (RRID:SCR_018213) Copy
http://treesoft.sourceforge.net/treebest.shtml
Software package to build, manipulate and display phylogenetic trees. Designed for building gene trees with known species tree and is highly efficient and accurate.
Proper citation: TreeBeST (RRID:SCR_018173) Copy
https://github.com/smajidian/phaseme
Software tool set to assess quality of per read phasing information and help to reduce errors during this process.
Proper citation: PhaseME (RRID:SCR_018739) Copy
https://www.biorxiv.org/content/10.1101/2020.09.24.311282v2.full
Software package to quickly transform microscope images into quality figures. User friendly tool for creating and formatting scientific figures, can export files into popular softwares like Adobe Illustrator, Microsoft Powerpoint, and Inkscape.
Proper citation: QuickFigures (RRID:SCR_019082) Copy
https://docs.conda.io/en/latest/
Software tool as cross platform, language agnostic binary package manager. Open source package management system and environment management system that runs on Windows, macOS and Linux. Can quickly install, run, and update packages and their dependencies. Package, dependency and environment management for any language—Python, R, Ruby, Lua, Scala, Java, JavaScript, C/ C++, FORTRAN, and more. Created for Python programs, but it can package and distribute software for any language. Conda can be combined with continuous integration systems such as Travis CI and AppVeyor to provide frequent, automated testing of your code. Conda package and environment manager is included in all versions of Anaconda and Miniconda.
Proper citation: Conda (RRID:SCR_018317) Copy
https://github.com/benmarwick/cvequality
Software R package contains functions to test for significant differences in coefficients of variation among multiple groups of observations.
Proper citation: cvequality (RRID:SCR_019124) Copy
https://github.com/ikmb/gwas-qc/
Software tool as scalable GWAS Quality Control pipeline for biobank scale datasets.
Proper citation: GWAS Quality Control Pipeline (RRID:SCR_019241) Copy
https://bioinf.shenwei.me/seqkit/
Software tool as cross platform and ultrafast toolkit for FASTA/Q file manipulation.
Proper citation: SeqKit (RRID:SCR_018926) Copy
https://CRAN.R-project.org/package=mHG
Software R package to run minimum hypergeometric test.
Proper citation: Minimum-Hypergeometric Test (RRID:SCR_018776) Copy
https://github.com/smithlabcode/riborex
Software R package for identification of differential translation from Ribo-seq data. Computational tool for mapping genome wide differences in translation efficiency.
Proper citation: riborex (RRID:SCR_019104) Copy
https://github.com/anuprulez/galaxy_tool_recommendation
Software developed by analyzing workflows composed by researchers on European Galaxy server, using deep learning approach. Used to recommend tools in Galaxy. Gated recurrent units neural network.
Proper citation: Tool recommender system in Galaxy (RRID:SCR_018491) Copy
https://github.com/DReichLab/AdmixTools
Software package that supports formal tests of whether admixture occurred, and makes it possible to infer admixture proportions and dates.
Proper citation: ADMIXTOOLS (RRID:SCR_018495) Copy
https://CRAN.R-project.org/package=openxlsx
Software R package to simplify creation of .xlsx files by providing high level interface to writing, styling and editing worksheets.
Proper citation: openxlsx (RRID:SCR_019185) Copy
https://github.com/dorianps/LESYMAP
Software R package to conduct lesion-to-symptom mapping from human MRI data.Takes lesion maps and cognitive performance scores from patients with stroke, and maps brain areas responsible for cognitive deficit.
Proper citation: LESYMAP (RRID:SCR_017967) Copy
https://hoohm.github.io/CITE-seq-Count/
Software python package that allows to count antibody TAGS from CITE-seq and/or cell hashing experiment. Software tool that allows to get UMI counts from single cell protein assay. Used to count (UMI counts) antibody-derived-tags (ADTs) or Cell Hashing tags (HTOs) in raw sequencing reads and build count matrix.
Proper citation: CITE-seq-Count (RRID:SCR_019239) Copy
https://github.com/dorianps/LINDA
Software R package for automated segmentation of chronic stroke lesions. Automated segmentation algorithm capable of learning relationship between existing manual segmentations and single T1-weighted MRI.
Proper citation: LINDA (RRID:SCR_017971) Copy
https://bioconductor.org/packages/release/bioc/html/MetaVolcanoR.html
Software R package to combine differential gene expression results. Differential expression meta analysis tool. Gene expression meta analysis visualization tool. Used to identify genes whose expression is consistently perturbed across several studies., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MetaVolcanoR (RRID:SCR_018549) Copy
Software Python package for Bayesian statistical modeling and probabilistic machine learning which focuses on advanced Markov chain Monte Carlo and variational fitting algorithms. Allows model specification directly in Python code.
Proper citation: PyMC3 (RRID:SCR_018547) Copy
https://w3.psychology.su.se/sleipner/
Software package as collection of modules implementing methods of analysis that form self-contained and empirically grounded toolbox for handling longitudinal data within person oriented paradigm.
Proper citation: sleipner (RRID:SCR_018143) Copy
Software Python package enabling Biological Expression Language to act as semantic integration layer for multi modal and multi scale data sets in life sciences. Used for integrating biological databases and structured data sources in BEL. Has ability to support curation of pathway mappings, integration of pathway databases, and machine learning applications.
Proper citation: Bio2BEL (RRID:SCR_017659) Copy
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