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https://github.com/HMPNK/CSA2.6

Software pipeline for high-throughput chromosome level vertebrate genome assembly. Pipeline, which after contig assembly performs post assembly improvements by ordering assembly and closing gaps, as well as splitting of low supported regions.

Proper citation: Chromosome Scale Assembler (RRID:SCR_017960) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/jupyter/jupyter_console

Terminal based console frontend for Jupyter kernels. This code is based on single process IPython terminal.

Proper citation: Jupyter-console (RRID:SCR_018414) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://nose.readthedocs.io/en/latest/

Software tool to extend unittest to make testing easier. Python unit test framework. Note, Nose has been in maintenance mode for the past several years and will likely cease without a new person/team to take over maintainership. New projects should consider using Nose2, py.test, or just plain unittest/unittest2.

Proper citation: Python Nose (RRID:SCR_018418) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://docs.pymc.io/

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   

•   Source: SciCrunch Registry

https://www.flidea.tech/flic-support

Software tool as user interface for running Fly Liquid Food Interaction Counter experiments.

Proper citation: FLIC Monitor (RRID:SCR_018387) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/bio2bel

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   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/org.Rn.eg.db/

Software R tool for genome wide annotation for Rat, primarily based on mapping using Entrez Gene identifiers.

Proper citation: org.Rn.eg.db (RRID:SCR_018358) Copy   

•   Source: SciCrunch Registry

https://woldlab.caltech.edu/wiki/Condor

Condor project maintains, distributes, and supports variety of computing systems that are deployed by commercial and academic interests world wide. Explores social and technical problems of cooperative computing on scales ranging from desktop to world wide computational Grid.

Proper citation: Condor (RRID:SCR_017664) Copy   

•   Source: SciCrunch Registry

https://github.com/dmis-lab/biobert

Pre-trained biomedical language representation model for biomedical text mining. This repository provides fine-tuning codes of BioBERT, language representation model for biomedical domain, especially designed for biomedical text mining tasks such as biomedical named entity recognition, relation extraction, question answering, etc.

Proper citation: BioBERT (RRID:SCR_017547) Copy   

•   Source: SciCrunch Registry

https://github.com/cobilab/geco3/

Software tool as DNA compressor that uses neural network to do mixing of experts.

Proper citation: GeCo3 (RRID:SCR_018877) Copy   

•   Source: SciCrunch Registry

https://www.openscad.org/

Software tool for creating solid 3D CAD objects. Used for creating 3D models focusing on CAD aspects of 3D modeling of machine parts. Reads in script file that describes object and renders 3D model from this script file.

Proper citation: OpenSCAD (RRID:SCR_018870) Copy   

•   Source: SciCrunch Registry