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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/STOmics/EAGS
Software tool for high resolved spatial transcriptomics. Smoothing approach for spatial transcriptome data with ultrahigh resolution. Used to determine neighborhood relationship of cells, to calculate smoothing contribution to recalculate the gene expression of each cell.
Proper citation: Efficient and Adaptive Gaussian Smoothing (RRID:SCR_024399) Copy
https://docs.igdiscover.se/en/stable/
Software to analyze antibody repertoires and discover new V genes from high-throughput sequencing reads.Heavy chains, kappa and lambda light chains are supported (to discover VH, VK and VL genes)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: IgDiscover (RRID:SCR_024037) Copy
https://github.com/sanger-pathogens/iva
Software tool as de novo assembler designed to assemble virus genomes that have no repeat sequences,using Illumina read pairs sequenced from mixed populations at extremely high and variable depth.
Proper citation: IVA (RRID:SCR_024044) Copy
https://github.com/bioinfo-ut/PlasmidSeeker
Software tool as k-mer based program for identification of known plasmids from whole genome sequencing reads. Used for identification of known plasmids from bacterial whole genome sequencing reads.
Proper citation: PlasmidSeeker (RRID:SCR_024167) Copy
https://github.com/babinyurii/recan
Software tool as genetic distance plotting for recombination events analysis.
Proper citation: recan (RRID:SCR_024317) Copy
https://github.com/mourisl/Lighter
Software tool as kmer-based error correction method for whole genome sequencing data. Lighter uses sampling rather than counting to obtain set of kmers that are likely from the genome. Using this information, Lighter can correct the reads containing sequence errors.
Proper citation: Lighter (RRID:SCR_024095) Copy
https://github.com/bkntr/brainways
Open source software that automatically registers coronal slices and quantifies fluorescent markers. Python based, AI registration algorithm for slice matching to the Waxholm rat atlas. Slice quantification can be trained on any atlas, which allows use for other subjects such as mice, zebrafish, and humans. AI-based software for registration and analysis of fluorescent markers on coronal brain slices.
Proper citation: Brainways (RRID:SCR_024402) Copy
http://rnainformatics.org.cn/RiboToolkit/
Integrated web server developed for Ribo-seq data analysis. Platform for analysis and annotation of ribosome profiling data to decode mRNA translation at codon resolution.Web based service to centralize Ribo-seq data analyses, including data cleaning and quality evaluation, expression analysis based on RPFs, codon occupancy, translation efficiency analysis, differential translation analysis, functional annotation, translation metagene analysis, and identification of actively translated ORFs.
Proper citation: RiboToolkit (RRID:SCR_024406) Copy
https://bioconductor.org/packages/ramr/
Software R package for detection of low frequency aberrant methylation events in large data sets obtained by methylation profiling using array or high-throughput bisulfite sequencing. Provides functions to visualize found aberrantly methylated regions, to generate sets of all possible regions to be used as reference sets for enrichment analysis, and to generate biologically relevant test data sets for performance evaluation of AMR/DMR search algorithms.
Proper citation: ramr (RRID:SCR_024408) Copy
https://github.com/bioinfo-center-pasteur-fr/toppred
Software tool for membrane protein structure prediction.Transmembrane topology prediction.Used for predicting topology of bacterial inner membrane proteins.
Proper citation: toppred (RRID:SCR_024385) Copy
http://www.nematodes.org/bioinformatics/trace2dbEST/
Software tool to process raw sequenceing chromatograph trace files from EST projects into quality checked sequences, ready for submission to dbEST.
Proper citation: trace2dbEST (RRID:SCR_024386) Copy
https://github.com/sina-cb/Tn-seqExplorer
Software package written in Java for analysis of high-throughput sequencing data of transposon mutant libraries.Reads the alignment and the gene annotation, and provides the user with set of tools to investigate data and identify possibly essential or advantageous genes as those that contain significantly low counts of transposon insertions.
Proper citation: Tn-seq explorer (RRID:SCR_024387) Copy
http://saclab.tamu.edu/essentiality/transit/
Software tool for Himar1 TnSeq analysis.Provides graphical interface to three different statistical methods for analyzing TnSeq data. Used for identifying essential genes in individual datasets as well as comparative analysis between conditions.
Proper citation: TRANSIT (RRID:SCR_024389) Copy
Software tool to reconstruct phylogenetic trees from molecular sequence data by maximum likelihood. Allows analysis of large data sets and automatically assigns estimations of support to each internal branch. Computes pairwise maximum likelihood distances as well as branch lengths for user specified trees.Conducts statistical tests on the data set.
Proper citation: TREE-PUZZLE (RRID:SCR_024382) Copy
https://rostlab.org/owiki/index.php/NORSp_-_predictor_of_NOn-Regular_Secondary_Structure
Online predictor of NOn-Regular Secondary Structure for disordered regions in protein. Used to predict long regions with no regular secondary structure. Upon user submission of protein sequence, NORSp will analyse the protein about its secondary structure, and presence of transmembrane helices and coiled-coil then return e-mail to user about the presence and position of disordered regions.
Proper citation: NORSp (RRID:SCR_024139) Copy
https://rostlab.org/owiki/index.php/Metastudent
Software tool to predict gene ontology terms for protein sequences through homology.
Proper citation: Metastudent (RRID:SCR_024110) Copy
https://github.com/Martinsos/edlib
Software C/C++ (and Python) library for sequence alignment using edit (Levenshtein) distance.
Proper citation: Edlib (RRID:SCR_024078) Copy
https://bitbucket.org/Glouvel/metabit/wiki/Home
Software pipeline for metagenomic and taxonomical analysis from shotgun sequencing.
Proper citation: metaBIT (RRID:SCR_024111) Copy
https://qtlreaper.sourceforge.net/
Software, written in C and compiled as Python module, for rapidly scanning microarray expression data for Quantitative Trait Locies. Searches for association between each expression trait and all genotypes and evaluates that association by permutation test. Performs bootstrap resampling to estimate confidence region for location of putative QTL.
Proper citation: qtlreaper (RRID:SCR_024199) Copy
https://mhap.readthedocs.io/en/stable/
Software tool as reference implementation of probabilistic sequence overlapping algorithm. Used to detect overlaps between noisy long-read sequence data.
Proper citation: MHAP (RRID:SCR_024113) Copy
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