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https://github.com/broadinstitute/pilon/

Software tool to automatically improve draft assemblies and find variation among strains, including large event detection. FASTA files of genome along with one or more BAM files of reads aligned as input. Read alignment analysis is used to identify inconsistencies between input genome and evidence in reads, then attempts to make improvements to genome.

Proper citation: Pilon (RRID:SCR_014731) Copy   

•   Source: SciCrunch Registry

https://brainiak.org

Open source software package of Python modules for neuroscience, primarily focused on functional Magnetic Resonance Imaging (fMRI) analysis. Used for analyzing neuroimaging data.

Proper citation: Brain Imaging Analysis Kit (RRID:SCR_014824) Copy   

•   Source: SciCrunch Registry

https://sanger-pathogens.github.io/Roary/

Software tool for rapid large scale prokaryote pan genome analysis. Builds large scale pan genomes, identifying core and accessory genes. Makes construction of pan genome of thousands of prokaryote samples on standard desktop without compromising on accuracy of results. Not intended for meta genomics or for comparing extremely diverse sets of genomes.

Proper citation: Roary (RRID:SCR_018172) Copy   

•   Source: SciCrunch Registry

https://ccb.jhu.edu/software/stringtie/

Software application for assembling of RNA-Seq alignments into potential transcripts. It enables improved reconstruction of a transcriptome from RNA-seq reads. This transcript assembling and quantification program is implemented in C++ .

Proper citation: StringTie (RRID:SCR_016323) Copy   

•   Source: SciCrunch Registry

http://web.stanford.edu/group/vista/cgi-bin/wiki/index.php/MrDiffusion

Software package for diffusion imaging analysis and visualization. Module of Vistasoft for processing diffusion weighted data and measuring and visualizing fractional anisotropy, mean diffusivity, axial and radial diffusivity, RGB fiber direction maps and analysis of MRI data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: MrDiffusion (RRID:SCR_016567) Copy   

•   Source: SciCrunch Registry

https://www.spyder-ide.org

Interactive scientific development environment package for Python. Used for editing, analysis, debugging, and profiling functionality of comprehensive development tool with data exploration, interactive execution, deep inspection, and visualization.

Proper citation: Spyder (RRID:SCR_017585) Copy   

•   Source: SciCrunch Registry

http://ikrsrv1.medma.uni-heidelberg.de/redmine/projects/ummperfusion

Analysis software for dynamic contrast enhanced magnetic resonance images with implementation of a pixel-by-pixel deconvolution approach. It quantifies T1-weighted contrast-enhanced dynamic MR imaging (DCE-MRI) perfusion data as an OsiriX plug-in.

Proper citation: UMMPerfusion (RRID:SCR_015970) Copy   

•   Source: SciCrunch Registry

https://rostlab.org/node/960

Alignment software for large-scale protein contact or protein-protein interaction prediction optimized for speed through shorter runtimes. FreeContact provides the opportunity to compute contact predictions in any environment (desktop or cloud).

Proper citation: FreeContact (RRID:SCR_016113) Copy   

•   Source: SciCrunch Registry

http://www.uimcimes.es/contenidos/golink?p=1

Software toolbox for Statistical Parametric Mapping (SPM) to fit reference-region kinetic models (SRTM, SRTM2, Patlak Reference and Logan Reference Plot) are currently available in QModeling to dynamic PET studies. Used for the analysis of brain imaging data sequences.

Proper citation: QModeling (RRID:SCR_016358) Copy   

•   Source: SciCrunch Registry

http://hms-dbmi.github.io/scde/index.html

Software package that implements a set of statistical methods for analyzing single-cell RNA-seq data, including differential expression analysis (Kharchenko et al.) and pathway and geneset overdispersion analysis (Fan et al.)

Proper citation: SCDE (RRID:SCR_015952) Copy   

•   Source: SciCrunch Registry

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

Software package for performing all stages of geometric morphometric shape analysis of landmark points and curves in 2-and-3-dimensions as well as 3D surfaces in the R statistical computing environment.

Proper citation: geomorph (RRID:SCR_016482) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.uni-muenster.de/tools/nanopipe2

Web tool for analysis of MinION (ONT) long sequencing reads. Used for analysis of reads generated by the Oxford Nanopore sequencing devices. Provides alignments to any target of interest, alignment statistics and information about polymorphisms.

Proper citation: NanoPipe (RRID:SCR_016852) Copy   

•   Source: SciCrunch Registry

https://www.uke.de/english/research/core-facilities/bioinformatics-core-en.html

Core provides bioinformatics services for researchers at University Medical Center Hamburg Eppendorf and related institutions. Focusing on high throughput sequencing data. Services include data analysis, consulting, software development, and bioinformatical training.

Proper citation: University Medical Center Hamburg-Eppendorf Bioinformatics Core Facility (RRID:SCR_017144) Copy   

•   Source: SciCrunch Registry

http://brainarchitecture.org/allen-atlas-brain-toolbox

Software Matlab toolbox for quantitative analysis of digitized brain wide gene expression data from Allen Atlas of adult mouse brain.

Proper citation: Brain Gene Expression Analysis toolbox (RRID:SCR_017438) Copy   

•   Source: SciCrunch Registry

http://biit.cs.ut.ee/graphweb/

GraphWeb allows the detection of modules from biological, heterogeneous and multi-species networks, and the interpretation of detected modules using Gene Ontology, cis-regulatory motifs and biological pathways. GraphWeb is a public web server for graph-based analysis of biological networks that: * analyses directed and undirected, weighted and unweighted heterogeneous networks of genes, proteins and microarray probesets for many eukaryotic genomes; * integrates multiple diverse datasets into global networks; * incorporates multispecies data using gene orthology mapping; * filters nodes and edges based on dataset support, edge weight and node annotation; * detects gene modules from networks using a collection of algorithms; * interprets discovered modules using Gene Ontology, pathways, and cis-regulatory motifs. Platform: Online tool

Proper citation: GraphWeb (RRID:SCR_005746) Copy   

•   Source: SciCrunch Registry

http://www.animalgenome.org/bioinfo/tools/catego/

CateGOrizer takes batch input of GO term IDs in a list format or unformatted plain text file, allows users to choose one of the available classifications such as GO_slim, GOA, EGAD, MGI_GO_slim, GO-ROOT, or a self-defined classification list, find its parental branch and performs an accumulative classification count, and returns the results in a sorted table of counts, percentages, and a pie chart (if it takes longer than standard time out period, it will email the user with a URL link to the results). This tool is comprised with a set of perl CGI programs coupled with a MySQL DBMS that stores the GO terms DAG data. Platform: Online tool

Proper citation: CateGOrizer (RRID:SCR_005737) Copy   

•   Source: SciCrunch Registry

http://report.nih.gov/

A database of federally funded biomedical research projects conducted at universities, hospitals, and other research institutions that provides a central point of access to reports, data, and analyses of NIH research. The RePORTER has replaced the CRISP database. The database, maintained by the Office of Extramural Research at the National Institutes of Health, includes projects funded by the National Institutes of Health (NIH), Substance Abuse and Mental Health Services (SAMHSA), Health Resources and Services Administration (HRSA), Food and Drug Administration (FDA), Centers for Disease Control and Prevention (CDCP), Agency for Health Care Research and Quality (AHRQ), and Office of Assistant Secretary of Health (OASH).

Proper citation: National Institutes of Health Research Portfolio Online Reporting Tool (RRID:SCR_006874) Copy   

•   Source: SciCrunch Registry

http://www.nlm.nih.gov/pubs/factsheets/medline.html

MEDLINE (Medical Literature Analysis and Retrieval System Online) is the U.S. National Library of Medicine''s (NLM) premier bibliographic database that contains over 16 million references to journal articles in life sciences with a concentration on biomedicine. MEDLINE is the primary component of PubMed, part of the Entrez series of databases provided by NLM''s National Center for Biotechnology Information (NCBI). MEDLINE may also be searched via the NLM Gateway. Currently, citations from approximately 5,200 worldwide journals in 37 languages; 60 languages for older journals. Citations for MEDLINE are created by the NLM, international partners, and collaborating organizations. The subject scope of MEDLINE is biomedicine and health, broadly defined to encompass those areas of the life sciences, behavioral sciences, chemical sciences, and bioengineering needed by health professionals and others engaged in basic research and clinical care, public health, health policy development, or related educational activities. MEDLINE also covers life sciences vital to biomedical practitioners, researchers, and educators, including aspects of biology, environmental science, marine biology, plant and animal science as well as biophysics and chemistry. Sponsors: Services/products providing access to MEDLINE data are also developed and made available by organizations that lease the database from NLM.

Proper citation: National Library of Health: Medical Literature Analysis and Retrieval System Online Fact Sheet (RRID:SCR_006994) Copy   

•   Source: SciCrunch Registry

http://pepr.cnmcresearch.org/

An experiment in web-database access to large multi-dimensional data sets using a standardized experimental platform to determine if the larger scientific community can be given simple, intuitive, and user-friendly web-based access to large microarray data sets. All data in PEPR is also available via NCBI GEO. The structure and goals of PEPR differ from other mRNA expression profiling databases in a number of important ways. * The experimental platform in PEPR is standardized, and is an Affymetrix - only database. All microarrays available in the PEPR web database should ascribe to quality control and standard operating procedures. A recent publication has described the QC/SOP criteria utilized in PEPR profiles ( The Tumor Analysis Best Practices Working Group 2004 ). * PEPR permits gene-based queries of large Affymetrix array data sets without any specialized software. For example, a number of large time series projects are available within PEPR, containing 40-60 microarrays, yet these can be simply queried via a dynamic web interface with no prior knowledge of microarray data analysis. * Projects in PEPR originate from scientists world-wide, but all data has been generated by the Research Center for Genetic Medicine, Children''''s National Medical Center, Washington DC. Future developments of PEPR will allow remote entry of Affymetrix data ascribing to the same QC/SOP protocols. They have previously described an initial implementation of PEPR, and a dynamic web-queried time series graphical interface ( Chen et al. 2004 ). A publication showing the utility of PEPR for pharmacodynamic data has recently been published ( Almon et al. 2003 ).

Proper citation: Public Expression Profiling Resource (RRID:SCR_007274) Copy   

•   Source: SciCrunch Registry

https://anvio.org

Open source software analysis and visualization platform for microbial omics including genomics, metagenomics, metatranscriptomics, pangenomics, metapangenomics, phylogenomics, and microbial population genetics in integrated fashion through extensive interactive visualization capabilities.

Proper citation: Anvi'o (RRID:SCR_021802) Copy   

•   Source: SciCrunch Registry