Tools   Select Another Resource Report Type

https://www.hiv.lanl.gov/catnap

Analyze a database of HIV-1 IC50 and IC80 neutralization data from publicly-available sources, in conjunction with HIV-1 Envelope sequences. Access to an extensive databases of information about neutralizing antibodies and viruses used in published neutralization studies. Tool interfaces also allow input and analysis of user data. PMID: 26044712, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CATNAP (RRID:SCR_016170) Copy   

•   Source: SciCrunch Registry

https://www.goldwave.com/goldwave.php

Software that enables users to digitally edit audio files. GoldWave can record, edit, and analyze audio for research-related purposes.

Proper citation: GoldWave (RRID:SCR_016189) Copy   

•   Source: SciCrunch Registry

http://www.xavierdidelot.xtreemhost.com/clonalframe.htm

Software package for the inference of bacterial microevolution using multilocus sequence data. It is used to identify the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance.

Proper citation: Clonalframe (RRID:SCR_016060) 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

http://www2.mrc-lmb.cam.ac.uk/relion

Software for determination of cryo-EM structures. It employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy.

Proper citation: RELION (RRID:SCR_016274) Copy   

•   Source: SciCrunch Registry

http://vensim.com/

Simulation software for improving the performance of real systems. Used for developing, analyzing, and packaging dynamic feedback models.

Proper citation: Vensim (RRID:SCR_016394) 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

https://www.genomics.agilent.com/article.jsp?pageId=2100

Software that performs data analysis algorithms for QPCR data. The software is included with the purchase of the Agilent MxPro QPCR System., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MxPro QPCR (RRID:SCR_016375) Copy   

•   Source: SciCrunch Registry

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

Data analysis software that can simultaneously characterize a large number of white matter bundles within and across different subjects for group analysis. It has three major components: construction of the structural connectome for the whole brain, low-dimensional representation of streamlines in each connection, and multi-level connectome analysis.

Proper citation: Mapping Population-based Structural Connectomes (RRID:SCR_016232) Copy   

•   Source: SciCrunch Registry

http://www.tdt.com/openex-suite.html

Software toolkit that is designed for configuration and control of TDT hardware. It can also display and analyze neurophysiology data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: OpenEx (RRID:SCR_016230) 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

https://github.com/nelpy

Software toolkit for neuroelectrophysiology object modeling and data analysis in Python. Open source Python package for analysis of neuroelectrophysiology data.

Proper citation: nelpy (RRID:SCR_016209) 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://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

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://lifebit.ai/

Platform for computing management for data analysis on the cloud from the Lifebit company. Allows the computational analyses to be permanently linked to live analyses pipelines.

Proper citation: Lifebit Deploit (RRID:SCR_016428) Copy   

•   Source: SciCrunch Registry