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http://biopp.univ-montp2.fr/wiki/index.php/Main_Page

Software providing a set of ready-to-use C++ libraries as re-usable tools to visualize, edit, print and output data for bioinformatics. It uses sequence analysis, phylogenetics, molecular evolution and population genetics to help to write programs., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Bio++ (RRID:SCR_016055) Copy   

•   Source: SciCrunch Registry

https://github.com/thegenemyers/DAZZ_DB

Software library and database to manage nucleotide sequencing read data. It stores the source Pacbio read information in such a way that it can re-create the original input data, thus permitting a user to remove the (effectively redundant) source files and avoid duplicating data.

Proper citation: Dazzler (RRID:SCR_016069) Copy   

•   Source: SciCrunch Registry

https://gotrack.msl.ubc.ca/

Open source web-based system and database that provides access to historical records and trends in the Gene Ontology (GO) and GO annotations (GOA). Used for monitoring changes in the Gene Ontology and their impact on genomic data analysis.

Proper citation: GOTrack (RRID:SCR_016399) Copy   

•   Source: SciCrunch Registry

https://www.icpsr.umich.edu/icpsrweb/content/addep/index.html

Provides access to data including wide range of topics related to disability. ADDEP data can be used to better understand and inform the implementation of Americans with Disabilities Act and other disability policies.

Proper citation: Archive of Data on Disability to Enable Policy (ADDEP) (RRID:SCR_016315) Copy   

•   Source: SciCrunch Registry

http://www.omicsbean.cn

Software tool for multi-omics data analysis that can perform complex and personalized analysis. Network regulation and molecular mechanism models can be customized according to the requirements of the users.

Proper citation: OmicsBean (RRID:SCR_016322) Copy   

•   Source: SciCrunch Registry

https://github.com/Sung-Huan/ANNOgesic

Software tool for bacterial/archaeal RNA-Seq based genome annotations. Used for integrating, detecting, predicting, and grouping RNA-Seq data.

Proper citation: ANNOgesic (RRID:SCR_016326) Copy   

•   Source: SciCrunch Registry

http://www.cycif.org/

Web page for cyclic immunofluorescence. It lists several downloadable data and software pertaining to cyclic immunofluorescence.

Proper citation: CycIF.org (RRID:SCR_016267) Copy   

•   Source: SciCrunch Registry

https://github.com/alesssia/YAMP

Software for processing and analysis of sequencing data. It has a strong focus on quality control, timely processing, functional annotation, and portability.

Proper citation: YAMP (RRID:SCR_016236) Copy   

•   Source: SciCrunch Registry

https://github.com/G-Node/nix/wiki

Software that defines a data model for annotated scientific datasets. It includes data together with metadata, and a corresponding file format based on HDF5 for storing and sharing such datasets.

Proper citation: NIX (RRID:SCR_016196) Copy   

•   Source: SciCrunch Registry

https://deeptools.readthedocs.io/en/develop/

Python based tools to process, visualize and analyse high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. Implemented within Galaxy framework. Used to perform complete bioinformatic workflows ranging from quality controls and normalizations of aligned reads to integrative analyses, including clustering and visualization approaches.

Proper citation: Deeptools (RRID:SCR_016366) Copy   

•   Source: SciCrunch Registry

https://github.com/sblanck/smagexp

Software toolkit for transcriptomics data meta-analysis. It integrates metaMA and metaRNAseq packages into Galaxy, carries out meta-analysis of gene expression data, handles microarray data from Gene Expression Omnibus (GEO) database, and more.

Proper citation: SMAGEXP (RRID:SCR_016360) Copy   

•   Source: SciCrunch Registry

http://uthscsa-imagetool.software.informer.com/

Image processing and analysis program for Windows 95 NT and has many of the same capabilities as NIH Image. ImageTool can acquire, display, edit, analyze, process, compress, save and print gray scale and color images.

Proper citation: UTHSCSA ImageTool (RRID:SCR_016208) Copy   

•   Source: SciCrunch Registry

https://www.xlstat.com/en/

Software for commercial data analysis and statistical software package for Microsoft Excel.

Proper citation: XLSTAT (RRID:SCR_016299) Copy   

•   Source: SciCrunch Registry

https://github.com/Teichlab/tracer

Software application for recovery of T cell receptor (TCR) data from single cell data. Used to reconstruct full-length, paired T cell receptor (TCR) sequences from T lymphocyte single-cell RNA sequence data. Links T cell specificity with functional response by revealing clonal relationships between cells alongside their transcriptional profiles.

Proper citation: TraCeR (RRID:SCR_016338) Copy   

•   Source: SciCrunch Registry

https://github.com/mikessh/migec

Software package for analysis of immune repertoire sequencing data. Used for recovery of T Cell Receptor ( TCR ) data from bulk population data.Used for high-throughput sequencing data analysis. Allows for error correction while preserving the natural diversity of complex immune repertoires.

Proper citation: migec (RRID:SCR_016337) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=clustree

Software package which allows to produce clustering trees and visualize clusterings at different resolutions. Used in the analysis of large data sets to group together samples with similar properties.

Proper citation: clustree (RRID:SCR_016293) Copy   

•   Source: SciCrunch Registry

http://www.flir.jp/instruments/display/?id=54865

Software application for thermography for FLIR Systems. It has a basic thermal image analysis function including color palette and image adjustment function. Used to analyse the thermographic measurement data.

Proper citation: FLIR tools (RRID:SCR_016330) Copy   

•   Source: SciCrunch Registry

https://hub.docker.com/r/biodepot/star-for-criu/

Software as an Hot Start software container for STAR alignment using CRIU (Checkpoint Restore in Userspace) tool to freeze the running container. Can be deployed to align RNA sequencing data. Used in the processing of biomedical big data for better reproducibility and reliability.

Proper citation: star-for-criu (RRID:SCR_016294) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/mica/

Software toolbox based on FSL command line tools that performs masked independent component analysis and related analyses in an integrated way within a spatially restricted subregion of the brain. Used for investigating functional connectivity in functional magnetic resonance imaging data in the field of neuroimaging.

Proper citation: masked ICA (mICA) Toolbox (RRID:SCR_016349) Copy   

•   Source: SciCrunch Registry

https://www.lungmap.net/

Portal for lung histochemistry data. For structural and molecular data regarding normal perinatal and postnatal lung development in the mouse and human. For public sharing of data sets, establishing a repository of young human lung tissues obtained through organ donor organizations, and developing a comprehensive lung ontology .Contains lung images and transcriptomic, proteomic, and lipidomic human and mouse data and provides scientific information to stimulate interest in research careers. Used to serve as a research resource and public education tool.

Proper citation: LungMap (RRID:SCR_016347) Copy   

•   Source: SciCrunch Registry