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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://pysam.readthedocs.io/en/latest/api.html
Software tool as interface for reading and writing SAM files. Python module to read and manipulate mapped short read sequence data stored in SAM/BAM files. Lightweight wrapper of htslib C-API.
Proper citation: pysam (RRID:SCR_021017) Copy
https://CRAN.R-project.org/package=caret
Software R package provides misc functions for training and plotting classification and regression models.Contains tools for data splitting, pre-processing, feature selection, model tuning using resampling, and variable importance estimation, as well as other functionality.
Proper citation: caret (RRID:SCR_021138) 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/ISA-tools/isa-api
Open platform for interoperable life science experimental metadata. Metadata framework as set of community specifications and software tools for enabling discovery, exchange and publication of metadata from experiments in life sciences. Python library for creation, editing, parsing, and validating of ISA-Tab and ISA-JSON formats.Provides programmatic metadata handling functionality to support automation, common interface and interoperable medium between two ISA formats, as well as with other life science data formats required for depositing data in public databases.
Proper citation: ISA API (RRID:SCR_020980) 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://github.com/cosanlab/facesync
Open source software Python toolbox which automatically synchronizes recorded facial expressions to videos and events such as social interactions.Framework for recording facial expressions with head mounted cameras.
Proper citation: FaceSync (RRID:SCR_021396) Copy
https://github.com/UmSenhorQualquer/d-track/blob/master/docs/source/index.rst
Software package to track object in 3D based on 3D schematics of scene.Semi automatic 3D video tracking technique to analyse movements and routines of aquatic animals with application to captive dolphins.
Proper citation: D-Track (RRID:SCR_021394) Copy
Open source software tool as file archiver with high compression ratio.
Proper citation: 7-Zip (RRID:SCR_021270) Copy
https://github.com/DeepLabCut/DeepLabCut
Open source software package for markerless pose estimation. 2D keypoint detection in animals.
Proper citation: DeepLabCut (RRID:SCR_021391) 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
https://github.com/hietakangas-laboratory/LAM
Software Python package for spatially defined cellular phenotyping using image segmentation data from linearizable tissue.Software quantitative phenotyping tool intended for regionally defined analysis of Drosophila midguts based on objects detected from microscopy images.
Proper citation: Linear Analysis of Midgut (RRID:SCR_021255) Copy
https://bioconductor.org/packages/EpiDISH/
Software R package provides tools to infer proportions of priori known cell-types present in sample representing mixture of such cell-types. Comparison of reference based algorithms for correcting cell-type heterogeneity in Epigenome-Wide Association Studies.
Proper citation: EpiDISH R package (RRID:SCR_018004) Copy
https://www.molinspiration.com/
Broad range of cheminformatics software tools supporting molecule manipulation and processing, including SMILES and SDfile conversion, normalization of molecules, generation of tautomers, molecule fragmentation, calculation of various molecular properties needed in QSAR, molecular modelling and drug design, high quality molecule depiction, molecular database tools supporting substructure and similarity searches. Molinspiration tools are platform independent and may be run on any PC, Mac, UNIX or LINUX machine. Software is distributed in form of engines, which may be used as stand-alone computational engines, used to power web-based tools, or incorporated into larger in-house Java applications.
Proper citation: Molinspiration (RRID:SCR_018525) Copy
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