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https://cran.r-project.org/web/packages/ggplot2/index.html

Open source software package for statistical programming language R to create plots based on grammar of graphics. Used for data visualization to break up graphs into semantic components such as scales and layers.

Proper citation: ggplot2 (RRID:SCR_014601) Copy   

•   Source: SciCrunch Registry
  

http://metastats.cbcb.umd.edu/detection.html

A statistical software package for comparing metagenomic datasets and clinical data sets comprised of two treatment populations, with each treatment population being made up of multiple samples. It relies on a non-parametric t-test.

Proper citation: Metastats (RRID:SCR_014610) Copy   

•   Source: SciCrunch Registry
  

http://www.openworm.org/

3D web browser that allows users to simulate and dissect virtual C. elegans. Users can explore the anatomy of a virtual, 3D worm by zooming in and out, rotating the model, and viewing the worm's different layers. NeuroML format and connector are used to enhance the simulation, and supporting programs and code are available for coders.

Proper citation: OpenWorm (RRID:SCR_014650) Copy   

•   Source: SciCrunch Registry
  

http://www.sci.utah.edu/software/fluorender.html

Interactive rendering tool for confocal microscopy data visualization. Combines rendering of multi-channel volume data and polygon mesh data, where properties of each dataset can be adjusted independently and quickly. Designed for neurobiologists, allowing them to better visualize confocal data from fluorescently-stained brains, but it is also useful for other biological samples. Features include feature tracking, 3D measurement tools, multiple render modes for multi-channel confocal data, and volume paint selection and segmentation.

Proper citation: FluoRender (RRID:SCR_014303) Copy   

•   Source: SciCrunch Registry
  

https://cmiclab.cs.ucl.ac.uk/CMIC/NiftyFit-Release

Software package for multi-parametric model-fitting of 4D Magnetic Resonance Imaging data. Software library to facilitate voxel wise fitting on a number of datatypes including T1 and T2 relaxometry, Arterial Spin Labeled MRI, Diffusion Weighted Imaging and Dynamic Contrast Enhanced MRI. T

Proper citation: NiftyFit (RRID:SCR_014301) Copy   

•   Source: SciCrunch Registry
  

http://darwin.uvigo.es/software/prottest_server.html

Web-based software used for the selection of best-fit models of protein evolution., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: ProtTest (RRID:SCR_014628) Copy   

•   Source: SciCrunch Registry
  

http://fatcat.burnham.org/

Web server for flexible protein structure comparison. Structure alignment is formulated as the aligned fragment pairs chaining process allowing at most t twists, and the flexible structure alignment is transformed into a rigid structure alignment when t is forced to be 0., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: FATCAT (RRID:SCR_014631) Copy   

•   Source: SciCrunch Registry
  

http://bioinfo.lifl.fr/RNA/sortmerna/

Sequence analysis software for filtering, mapping and OTU-picking NGS reads. SortMeRNA takes as input a file of reads (fasta or fastq format) and one or multiple rRNA database file(s), and sorts apart rRNA and rejected reads into two files specified by the user., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SortMeRNA (RRID:SCR_014402) Copy   

•   Source: SciCrunch Registry
  

http://compbio.mit.edu/cummeRbund/index.html

Software R package used for simplifying and analyzing Cufflink RNA-Seq output. This program takes various output files from a cuffdiff run and creates a SQLite database of the results that will describe the appropriate relationships between the genes, transcripts, transcription start sites and CDS regions.

Proper citation: CummeRbund (RRID:SCR_014568) Copy   

•   Source: SciCrunch Registry
  

Ratings or validation data are available for this resource

http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Quality control software that perform checks on raw sequence data coming from high throughput sequencing pipelines. This software also provides a modular set of analyses which can give a quick impression of the quality of the data prior to further analysis.

Proper citation: FastQC (RRID:SCR_014583) Copy   

•   Source: SciCrunch Registry
  

http://www.matrixscience.com/server.html

A software package and server used to identify and characterize proteins from primary sequence databases using mass spectrometry data. Mascot integrates peptide mass fingerprinting, sequence querying, and MS/MS ion searching in order to search for proteins in databases like SwissProt, NCBInr, EMBL EST divisions, contaminants, and cRAP. If a license is purchased, users may: search data sets that exceed the 1200 spectrum limit of the free version; set up automated, high throughput work; add and edit proteins and quantification methods; and search a preferred collection of sequence databases. The software package works with instruments from AB Sciex, Agilent, Bruker, Jeol, Shimadzu, Thermo Scientific, and Waters.

Proper citation: Mascot (RRID:SCR_014322) Copy   

•   Source: SciCrunch Registry
  

http://www.gromacs.org

Software package created to perform molecular dynamics. Molecular dynamics package mainly designed for simulations of proteins, lipids, and nucleic acids. Can also be used for research on non-biological systems, such as polymers.

Proper citation: GROMACS (RRID:SCR_014565) Copy   

•   Source: SciCrunch Registry
  

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

Framework for exploring genetic variation in the context of the genome annotations available for the human genome. Users can load a VCF file into a database and each variant is automatically annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks, OMIM, dbSNP, KEGG, and HPRD.

Proper citation: GEMINI (RRID:SCR_014819) Copy   

•   Source: SciCrunch Registry
  

http://abacus.gene.ucl.ac.uk/software/paml.html

Package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. PAML estimates parameters and tests hypotheses to study the evolutionary process from a phylogenetic tree., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PAML (RRID:SCR_014932) Copy   

•   Source: SciCrunch Registry
  

http://regulatorygenomicsgroup.org/chicago

Statistical pipeline for detecting significant chromosomal interactions in Capture Hi-C data. CHiCAGO uses a convolution background model accounting for both random Brownian collisions between chromatin fragments and technical noise. CHiCAGO then performs a p-value weighting procedure based on the expected true positive rates at different distance ranges, with scores representing soft-thresholded -log weighted p-values., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: CHiCAGO (RRID:SCR_014941) Copy   

•   Source: SciCrunch Registry
  

https://github.com/BGI-flexlab/SOAPnuke

Multi-threaded software for rapid quality control and preprocessing of high throughput sequencing data specified for different experiments. It consists of four modules that speed up the report on statistics graphs of raw datasets, preprocessed datasets and preprocessing status.

Proper citation: SOAPnuke (RRID:SCR_015025) Copy   

•   Source: SciCrunch Registry
  

http://bowtie-bio.sourceforge.net/bowtie2/index.shtml

Ultrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method.

Proper citation: Bowtie 2 (RRID:SCR_016368) Copy   

•   Source: SciCrunch Registry
  

http://dgrapov.github.io/MetaMapR/

An open-source software program for integrating enzymatic transformations with metabolite structural similarity, mass spectral similarity and empirical associations to generate connected metabolic networks and display results using data visualization techniques.

Proper citation: MetaMapR (RRID:SCR_014685) Copy   

•   Source: SciCrunch Registry
  

http://amp.pharm.mssm.edu/gen3va/

Software tool for aggregation and analysis of gene expression signatures from related studies.Used to aggregate and analyze gene expression signatures extracted from GEO by crowd using GEO2Enrichr. Used to view aggregated report that provides global, interactive views, including enrichment analyses, for collections of signatures from multiple studies sharing biological theme.

Proper citation: GEN3VA (RRID:SCR_015682) Copy   

•   Source: SciCrunch Registry
  

https://cm.jefferson.edu/Off-Spotter//

Web application that identifies genomic instances for a given combination of gRNA(s), PAM, number of mismatches, and seed. This tool is limited to a single 1,000 nucleotides sequence or fewer than twenty CR-separated 20-mers.

Proper citation: Off-Spotter (RRID:SCR_015739) Copy   

•   Source: SciCrunch Registry