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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://github.com/ANGSD/ngsRelate
Software tool for estimating pairwise relatedness from next-generation sequencing data.
Proper citation: ngsRelate (RRID:SCR_016588) Copy
https://bioconductor.org/packages/release/bioc/html/ComplexHeatmap.html
Software package to arrange multiple heatmaps and support various annotation graphics. Used to visualize associations between different sources of data sets and to reveal potential patterns.
Proper citation: ComplexHeatmap (RRID:SCR_017270) Copy
https://swissmodel.expasy.org/
Software tool as fully automated protein structure homology modeling server, accessible via ExPASy web server, or from program DeepView Swiss Pdb-Viewer. Structural bioinformatics web-server dedicated to homology modeling of 3D protein structures. Used to make protein modelling accessible to all biochemists and molecular biologists.
Proper citation: SWISS-MODEL (RRID:SCR_018123) Copy
https://github.com/lkmklsmn/DrivAER
Software tool as method for identification of driving transcriptional programs based on AutoEncoder derived Relevance scores. Infers relevance scores for transcriptional programs with respect to specified outcomes of interest in single-cell RNA sequencing data, such as psuedotemporal ordering or disease status.Used for manifold interpretation in scRNA-seq data.
Proper citation: DrivAER (RRID:SCR_019076) Copy
http://www.imgt.org/HighV-QUEST/home.action
Next generation B and T cell sequence alignment and characterization online surface by IMGT. Web portal for immunoglobulin (IG) or antibody and T cell receptor (TR) analysis from NGS high throughput and deep sequencing.
Proper citation: IMGT HighV-QUEST (RRID:SCR_018196) Copy
https://pm4ngs.readthedocs.io/
Software tool to generate standard organizational structure for Next Generation Sequencing data analysis. Includes directory structure for project, several Jupyter notebooks for data management and CWL workflows for pipeline execution.
Proper citation: PM4NGS (RRID:SCR_019164) Copy
Software application to organize and store in structured format signaling information published in scientific literature. Information is stored as binary causative relationships between biological entities and can be represented graphically as activity flow. Each relationship is linked to literature reporting experimental evidence. Each node is annotated with chemical inhibitors that modulate its activity. Signaling information is mapped to human proteome. SIGNOR 2.0 stores manually annotated causal relationships between proteins and other biologically relevant entities including chemicals, phenotypes, complexes, etc with compliance to FAIR data principles.
Proper citation: SIGNOR (RRID:SCR_018485) Copy
A web application to assist in the identification of articles and research related to literature search terms. The search covers full text articles in the Europe PMC repository. Relevant papers are suggested to users based on the scientific term searched and the selection of questions, generated by the application, relevant to term searched.
Proper citation: EvidenceFinder (RRID:SCR_013764) Copy
Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron.
Proper citation: MRIcron (RRID:SCR_002403) Copy
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
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
https://edspace.american.edu/openbehavior/project/facesync/, https://bio.tools/FaceSync
Project related to emotions and facial expressions. Includes open source guide to building affordable head mount for camera to maintain high temporal and spatial resolution of face throughout duration of experiment. Device is paired with FaceSync, Python toolbox which automatically synchronizes recorded facial expressions to videos and events such as social interactions.
Proper citation: FaceSync project (RRID:SCR_021393) Copy
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
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
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
http://zzlab.net/blink/index.html
Software for next level of genome wide association studies with both individuals and markers in millions. The method releases the requirement that causative genes are evenly distributed on genome and consequently boosts statistical power.
Proper citation: BLINK (RRID:SCR_016288) Copy
http://bioconductor.org/packages/release/bioc/html/MetaCyto.html
Software tool for automated meta-analysis of mass and flow cytometry data. Provides functions for preprocessing, automated gating and meta-analysis of cytometry data and collection of cytometry data from the ImmPort database.
Proper citation: MetaCyto (RRID:SCR_016415) Copy
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
https://omictools.com/fluxmodecalculator-tool
Software for performing flux mode analysis in stoichiometric models. FluxModeCalculator enables large-scale elementary flux mode (EFM) computation and uses the OpenMP API to optimally exploit processor architectures with multiple cores., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: FluxModeCalculator (RRID:SCR_016290) Copy
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
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