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http://amp.pharm.mssm.edu/X2K/

Software tool to produce inferred networks of transcription factors, proteins, and kinases predicted to regulate the expression of the inputted gene list by combining transcription factor enrichment analysis, protein-protein interaction network expansion, with kinase enrichment analysis. It provides the results as tables and interactive vector graphic figures.

Proper citation: eXpression2Kinases (RRID:SCR_016307) Copy   

•   Source: SciCrunch Registry

http://abacas.sourceforge.net

Software that contiguates (align, order, orientate), visualizes and designs primers to close gaps on shotgun assembled contigs based on a reference sequence. ABACAS finds alignment positions and identifies syntenies of assembled contigs against the reference, then generates a pseudomolecule taking overlapping contigs and gaps into account.

Proper citation: ABACAS (RRID:SCR_015852) Copy   

•   Source: SciCrunch Registry

http://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMAINATRIX

Software for protein domain search. It is a part of Embassy software package.

Proper citation: DOMAINATRIX (RRID:SCR_016084) Copy   

•   Source: SciCrunch Registry

https://git.metabarcoding.org/obitools/ecopcr/wikis/home

Software for Electronic PCR that estimates PCR barcode primers quality and develops new barcode primers. In conjunction with OBITools, users can postprocess ecoPCR output to compute barcode coverage and barcode specificity., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Ecopcr (RRID:SCR_016082) Copy   

•   Source: SciCrunch Registry

https://github.com/rbutleriii/Clinotator

Software that performs clinical interpretation of ambiguous ClinVar annotations. This software takes batches of variants as input and queries NCBI eutilities to generate scoring metrics.

Proper citation: Clinotator (RRID:SCR_016054) Copy   

•   Source: SciCrunch Registry

https://qgis.org/en/site/

Open source cross platform desktop geographic information system application that supports viewing, editing, and analysis of geospatial data. Functions as geographic information system software, allowing users to analyze and edit spatial information, in addition to composing and exporting graphical maps.

Proper citation: QGIS (RRID:SCR_018507) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/Bio-ASN1-EntrezGene

Software regular expression based Perl Parser for NCBI Entrez Gene genome databases. Parses ASN.1-formatted Entrez Gene record and returns data structure that contains all data items from gene record.

Proper citation: Bio-ASN1-EntrezGene (RRID:SCR_024056) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/AcePerl

Software provides an interface to the ACEDB object-oriented database. Both read and write access is provided, and ACE objects are returned as similarly-structured Perl objects. Multiple databases can be opened simultaneously.

Proper citation: AcePerl (RRID:SCR_024057) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/Bio-SamTools

Software Perl interface to SamTools library for DNA sequencing.

Proper citation: Bio-SamTools (RRID:SCR_024066) Copy   

•   Source: SciCrunch Registry

https://metacpan.org/dist/Bio-SCF

Software Perl extension for reading and writting SCF sequence files.This module provides Perl interface to SCF DNA sequencing files. It has both tied hash and an object-oriented interfaces. It provides the ability to read fields from SCF files and limited ability to modify them and write them back.

Proper citation: Bio-SCF (RRID:SCR_024068) Copy   

•   Source: SciCrunch Registry

https://github.com/COMBINE-lab/pufferfish

Software tool implementing novel indexing data structure for compacted de Bruijn graph and colored compacted de Bruijn graph.

Proper citation: pufferfish (RRID:SCR_024184) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.org/biococoa/

Open source framework for bioinformatics written in Objective-C. Provides Cocoa and GNUstep programmers with full suite of APIs for handling and manipulating biological sequences.

Proper citation: BioCocoa (RRID:SCR_023977) Copy   

•   Source: SciCrunch Registry

http://biblatex-biber.sourceforge.net/

Software bibliography processing backend for LaTeX biblatex package. Supports unsurpassed feature set for automated conformance to complex bibliography style requirements such as labelling, sorting and name handling. BibTeX replacement for users of BibLaTeX.

Proper citation: Biber (RRID:SCR_023973) Copy   

•   Source: SciCrunch Registry

https://camitk.imag.fr/

Software Computer Assisted Medical Intervention Tool Kit helps researchers and clinicians to easily and rapidly collaborate in order to prototype CAMI applications, that feature medical images, surgical navigation and biomechanical simulations.Open source, cross-platform generic tool, written in C++, which can handle medical images, surgical navigations and biomechanical simulations.

Proper citation: CamiTK (RRID:SCR_023984) Copy   

•   Source: SciCrunch Registry

https://github.com/walaj/SeqLib

Software C++ htslib/bwa-mem/fermi interface for interrogating sequence data

Proper citation: SeqLib (RRID:SCR_024091) Copy   

•   Source: SciCrunch Registry

http://johnhommer.com/academic/code/aghermann

Sotware tool designed to run Process S simulations on Slow Wave Activity profiles from human EEG recordings.Produces set of sleep homeostat parameters which can be used to describe and differentiate individual sleepers, such as short vs long sleepers, early vs late, etc.Sleep research experiment manager, with facility for reading, displaying, and manual and semi-automatic scoring EEG recordings in edf format; conventional PSD and EEG Microcontinuity profiles; artifact detection; Independent Component Analysis; basic sleep analysis NREM-REM cycle detection.

Proper citation: Aghermann (RRID:SCR_023965) Copy   

•   Source: SciCrunch Registry

https://github.com/gem-pasteur/macsyfinder

Software tool to mine genomes for molecular systems with Application to CRISPR-Cas Systems. Detection of macromolecular systems in protein datasets using systems modelling and similarity search.

Proper citation: MacSyFinder (RRID:SCR_024106) Copy   

•   Source: SciCrunch Registry

https://github.com/mateidavid/nanocall

Software basecaller for Oxford Nanopore Technologies sequencing data. Oxford Nanopore Basecaller.

Proper citation: Nanocall (RRID:SCR_024124) Copy   

•   Source: SciCrunch Registry

https://odelaneau.github.io/shapeit4/

Software tool for estimation of haplotypes aka phasing for SNP array and high coverage sequencing data. The version 4 is refactored and improved version of SHAPEIT algorithm with multiple key additional features.

Proper citation: shapeit4 (RRID:SCR_024335) Copy   

•   Source: SciCrunch Registry

https://www.cs.cmu.edu/~ckingsf/software/sailfish/

Software tool that implements novel, alignment free algorithm for estimation of isoform abundances directly from set of reference sequences and RNA-seq reads.

Proper citation: sailfish (RRID:SCR_024326) Copy   

•   Source: SciCrunch Registry