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https://jtremblay.github.io/amplicontagger.html

Software tool as rRNA marker gene amplicon pipeline coded in python framework that enables fine tuning and integration of virtually any potential rRNA gene amplicon bioinformatic procedure. Designed to work within HPC environment, supporting complex network of job dependencies with smart restart mechanism in case of job failure or parameter modifications.

Proper citation: AmpliconTagger (RRID:SCR_019112) Copy   

•   Source: SciCrunch Registry

https://nanopore.usegalaxy.eu/

Webserver to process, analyse and visualize Oxford Nanopore Technologies (ONT) data and similar long-reads technologies. Collection of best practice and popular ONT-oriented tools are integrated in this custom Galaxy instance.

Proper citation: NanoGalaxy (RRID:SCR_018912) Copy   

•   Source: SciCrunch Registry

https://nrdg.github.io/fracridge

Software tool as regularization technique that penalizes L2-norm of coefficients in linear regression. Available in two programming languages MATLAB and Python.

Proper citation: fracridge (RRID:SCR_019045) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/synergyfinder/

Software R package as efficient implementations for all popular synergy scoring models for drug combinations, including HSA, Loewe, Bliss and ZIP and visualization of synergy scores as either two dimensional or three dimensional interaction surface over dose matrix. Used to calculate and visualize synergy scores for drug combinations.

Proper citation: SynergyFinder (RRID:SCR_019318) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/fgsea/

Software R package for fast preranked gene set enrichment analysis. Allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.

Proper citation: fgsea (RRID:SCR_020938) Copy   

•   Source: SciCrunch Registry

https://github.com/pensoft/omicsdatapaper

Software package for streamlined import of omics metadata from European Nucleotide Archive into OMICS Data Paper manuscript. Omics Data Paper R Shiny app demonstrates workflow for automatic import of ENA genomic metadata into omics data paper manuscript. Streamlined conversion of metadata into manuscript facilitates authoring of omics data papers, which allow omics dataset creators to receive credit for their work and to improve description and visibility of their datasets.

Proper citation: Omics Data Paper Generator (RRID:SCR_019809) Copy   

•   Source: SciCrunch Registry

https://github.com/slzarate/parliament2

Software tool to identify structural variants in given sample relative to reference genome. Runs combination of tools to generate structural variant calls on whole genome sequencing data.

Proper citation: Parliament2 (RRID:SCR_019187) Copy   

•   Source: SciCrunch Registry

https://sydneybiox.github.io/CiteFuse/

Software R package consisting of suite of tools for doublet detection, modality integration, clustering, differential RNA and protein expression analysis, antibody-derived tag evaluation, ligand-receptor interaction analysis and interactive web-based visualization of CITE-seq data.

Proper citation: CiteFuse (RRID:SCR_019321) Copy   

•   Source: SciCrunch Registry

https://guoweilong.github.io/BS_Seeker2/index.html

Software tool as versatile aligning pipeline for bisulfite sequencing data. Used for mapping bisulfite sequencing data and generating DNA methylomes. Improves mappability over existing aligners by using local alignment. Maps reads from RRBS library by building special indexes with improved efficiency and accuracy. Provides additional function for filtering out reads with incomplete bisulfite conversion, which is useful in minimizing overestimation of DNA methylation levels.

Proper citation: Bs-Seeker2 (RRID:SCR_020948) Copy   

•   Source: SciCrunch Registry

https://github.com/pavanvidem/chira

Software tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.

Proper citation: ChiRA (RRID:SCR_019219) Copy   

•   Source: SciCrunch Registry

https://github.com/cmayer/BaitFisher-package

Software toolkit for multispecies target DNA enrichment probe design. It consists of two programs: BaitFisher and BaitFilter, which are designed to construct hybrid enrichment baits for multiple sequence alignments or annotated features in multiple sequence alignments.

Proper citation: Baitfisher (RRID:SCR_015985) Copy   

•   Source: SciCrunch Registry

http://avogadro.cc/

Software for semantic chemical editing, visualization, and analysis. It is designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas.

Proper citation: Avogadro (RRID:SCR_015983) Copy   

•   Source: SciCrunch Registry

https://github.com/sanger-pathogens/Bio-Tradis

Analysis software for the output from TraDIS (Transposon Directed Insertion Sequencing) analyses of dense transposon mutant libraries. The Bio-Tradis analysis pipeline is implemented as an extensible Perl library which can either be used as is, or as a basis for the development of more advanced analysis tools.

Proper citation: Bio-tradis (RRID:SCR_015993) Copy   

•   Source: SciCrunch Registry

http://www.vicbioinformatics.com/software.barrnap.shtml

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software to predict the location of ribosomal RNA genes in genomes. It supports bacteria, archaea, mitochondria, and eukaryotes. It takes FASTA DNA sequence as input, writes GFF3 as output, and supports multithreading., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Barrnap (RRID:SCR_015995) Copy   

•   Source: SciCrunch Registry

http://fastml.tau.ac.il/

Web application for the reconstruction of ancestral sequences. It computes maximum likelihood ancestral sequence reconstruction based on the phylogenetic relations between homologous sequences.

Proper citation: Fastml (RRID:SCR_016092) Copy   

•   Source: SciCrunch Registry

http://standage.github.io/AEGeAn

Software toolkit for the analysis and evaluation of genome annotations. The toolkit includes a variety of analysis programs, e.g. for comparing distinct sets of gene structure annotations (ParsEval), computation of gene loci (LocusPocus) and more.

Proper citation: Aegean (RRID:SCR_015965) Copy   

•   Source: SciCrunch Registry

https://github.com/EvolBioInf/andi

Software tool for rapidly computing and estimating evolutionary distance between closely related genomes. Because andi does not compute full alignments it scales even up to thousands of bacterial genomes.

Proper citation: andi (RRID:SCR_015971) Copy   

•   Source: SciCrunch Registry

http://www.zucic.org/garlic/

Software application for visualization and editing of biomolecules. Used for the investigation of membrane proteins, visualization of other proteins and geometric objects, and analysis of protein sequences.

Proper citation: Garlic (RRID:SCR_016118) Copy   

•   Source: SciCrunch Registry

http://www.gamgi.org/

Software application which provides a graphical interface to build, view and analyze atomic structures. It provides a graphical interface to study atomic structures, to prepare images for presentations, and teach the atomic structure of matter.

Proper citation: Gamgi (RRID:SCR_016116) Copy   

•   Source: SciCrunch Registry

http://disulfind.dsi.unifi.it/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023, Software for predicting the disulfide bonding state of cysteines and their disulfide connectivity, starting from a protein sequence alone and may be useful in other genomic annotation tasks.

Proper citation: DISULFIND (RRID:SCR_016072) Copy   

•   Source: SciCrunch Registry