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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   

•   Source: SciCrunch Registry

https://glimmpse.samplesizeshop.org/#/

Web based software tool that calculates power and sample size for study designs with normally distributed outcomes. Permits power calculations for clinical trials, randomized experiments, and observational studies with clustering, repeated measures, and both, and almost any testable hypothesis. GLIMMPSE Version 3 release back end has been refactored in Python, interface has been simplified, requiring user decisions about only one topic per screen, new menu improves specification of both between-participant and within-participant hypothese, recursive algorithm permits computing covariances for up to ten levels of clustering., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GLIMMPSE (RRID:SCR_016297) Copy   

•   Source: SciCrunch Registry

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

R package from CRAN to extract and visualize the results of multivariate data analysis.

Proper citation: factoextra (RRID:SCR_016692) Copy   

•   Source: SciCrunch Registry

https://github.com/lufuhao/Gsnap2Augustus

Software tool to generate hints for Augustus in ab initio gene prediction using 2 step mapping by Gsnap.

Proper citation: Gsnap2Augustus (RRID:SCR_017555) Copy   

•   Source: SciCrunch Registry

https://github.com/sreeramkannan/Shannon

Software tool for de novo transcriptome assembly from RNA-Seq data.

Proper citation: Shannon (RRID:SCR_017037) Copy   

•   Source: SciCrunch Registry

https://github.com/neurostuff/NiMARE

Software Python package for coordinate and image based meta analysis of neuroimaging data.

Proper citation: NiMARE (RRID:SCR_017398) Copy   

•   Source: SciCrunch Registry

https://www.iconplc.com/innovation/nonmem/

Software tool for nonlinear mixed effects modelling. Used for population pharmacokinetic and pharmacodynamic analysis and to simulate data and to fit data. Used in the development of new drugs. NONMEM versions up through 6 are the property of the Regents of the University of California, San Francisco, but ICON Development Solutions has exclusive rights to license their use. NONMEM 7 up to the current version is the property of ICON Development Solutions.

Proper citation: NONMEM (RRID:SCR_016986) Copy   

•   Source: SciCrunch Registry

https://github.com/ANGSD/ngsRelate

Software tool for estimating pairwise relatedness from next-generation sequencing data.

Proper citation: ngsRelate (RRID:SCR_016588) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/HajkD/LTRpred

Software package for automated functional annotation of LTR retrotransposons for comparative genomics studies. Used to perform de novo functional annotation of LTR retrotransposons from any genome assembly in fasta format.

Proper citation: LTRpred (RRID:SCR_017031) Copy   

•   Source: SciCrunch Registry

https://shimadzu.com.au/labsolutions

Software package for data analysis by Shimadzu Oceania.

Proper citation: LabSolutions (RRID:SCR_018241) Copy   

•   Source: SciCrunch Registry

https://software.broadinstitute.org/cancer/cga/polysolver

Software tool for HLA typing based on whole exome sequencing data and infers alleles for three major MHC class I genes. Enables accurate inference of germline alleles of class I HLA-A, B and C genes and subsequent detection of mutations in these genes using inferred alleles as reference.

Proper citation: Polysolver (RRID:SCR_022278) Copy   

•   Source: SciCrunch Registry

https://github.com/mrcgndr/plant_cataloging_workflow

Software workflow for automatized spatio temporal plant positioning based on UAV images.

Proper citation: Plant Cataloging Workflow (RRID:SCR_022276) Copy   

•   Source: SciCrunch Registry

https://maayanlab.cloud/sigcom-lincs

Web server that serves over million gene expression signatures processed, analyzed, and visualized from LINCS, GTEx, and GEO. Data and metadata search engine for gene expression signatures.

Proper citation: SigCom LINCS (RRID:SCR_022275) Copy   

•   Source: SciCrunch Registry

http://kinefold.curie.fr/

Web service for RNA/DNA folding predictions including pseudoknots and entangled helices.Used for prediction and statistics of pseudoknots in RNA structures using exactly clustered stochastic simulations.

Proper citation: KineFold (RRID:SCR_022273) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=emmeans

Software R package to obtain estimated marginal means for linear, generalized linear, and mixed models. Compute contrasts or linear functions of EMMs, trends, and comparisons of slopes. Plots and other displays.

Proper citation: emmeans (RRID:SCR_018734) Copy   

•   Source: SciCrunch Registry

https://www2.hhu.de/rna/html/hexplorer_score.php

Web tool for genomic HEXploring allows landscaping of novel potential splicing regulatory elements. Allows landscaping of splicing regulatory regions, provides quantitative measure of mutation effects on splice enhancing and silencing properties and permitts calculation of mutationally most effective nucleotide.

Proper citation: HEXplorer score (RRID:SCR_022269) Copy   

•   Source: SciCrunch Registry

http://www.codons.org/calc.html

Software tool for calculating and comparing synonymous codon usage and its impact on protein folding. Used to harmonize codon usage frequencies for heterologous gene expression. Codon usage calculator that evaluates relative usage frequencies of synonymous codons used to encode protein sequence of interest and compares these results to rigorous null mode.Evaluates synonymous codon usage patterns for any coding sequence from any fully sequenced genome.

Proper citation: %MinMax (RRID:SCR_022268) Copy   

•   Source: SciCrunch Registry

https://github.com/slimsuite/diploidocus

Software package for diploid genome assembly analysis. Sequence analysis toolkit for number of different analyses related to diploid genome assembly.

Proper citation: Diploidocus (RRID:SCR_021231) Copy   

•   Source: SciCrunch Registry