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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Megraft Resource Report Resource Website |
Megraft (RRID:SCR_000240) | Megraft | software resource | A software package to graft ribosomal small subunit (16S/18S) fragments onto full-length sequences for accurate species richness and sequencing depth analysis in pyrosequencing-length metagenomes. | windows, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:22824070 | Free, Available for download, Freely available | biotools:megraft, OMICS_02161 | https://bio.tools/megraft | SCR_000240 | 2026-02-14 01:59:39 | 0 | ||||||
|
VARiD Resource Report Resource Website |
VARiD (RRID:SCR_000241) | VARiD | software resource | Software using a Hidden Markov Model for SNP (single nucleotide polymorphism) and indel identification with AB-SOLiD color-space as well as regular letter-space reads. | c, single nucleotide polymorphism, indel, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Toronto; Ontario; Canada |
PMID:20529926 | Free, Available for download, Freely available | OMICS_02163, biotools:varid | https://bio.tools/varid | SCR_000241 | 2026-02-14 01:59:40 | 0 | ||||||
|
TAPIR: target prediction for plant microRNAs Resource Report Resource Website 10+ mentions |
TAPIR: target prediction for plant microRNAs (RRID:SCR_000237) | TAPIR | Web server designed for prediction of plant microRNA targets. | prediction of plant microRNA targets, microrna, target, fasta, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Ghent University; Ghent; Belgium has parent organization: VIB; Flanders; Belgium |
PMID:20430753 | biotools:tapir, OMICS_04004 | https://bio.tools/tapir | SCR_000237 | 2026-02-14 01:59:39 | 10 | ||||||||
|
SODOCK Resource Report Resource Website 1+ mentions |
SODOCK (RRID:SCR_000193) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. An optimization algorithm based on particle swarm optimization (PSO) for solving flexible protein-ligand docking problems. | particle swarm optimization, protein, ligand, docking, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: National Chiao Tung University; Hsinchu; Taiwan |
PMID:17186483 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:sodock, OMICS_01606 | https://bio.tools/sodock | SCR_000193 | 2026-02-14 01:59:38 | 1 | |||||||
|
Quant Resource Report Resource Website |
Quant (RRID:SCR_000267) | software resource | A software tool for the proteomics community that may help improving analysis of proteomic experimental data. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:17584939 | Free, Available for download, Freely available | OMICS_02504, biotools:quant | https://bio.tools/quant | SCR_000267 | 2026-02-14 01:59:40 | 0 | |||||||
|
PeptideProphet Resource Report Resource Website 1+ mentions |
PeptideProphet (RRID:SCR_000274) | software resource | Software that automatically validates peptide assignments to MS/MS spectra made by database search programs such as SEQUEST. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: SourceForge |
PMID:12403597 | Free, Available for download, Freely available | OMICS_02520, biotools:peptideprophet | https://bio.tools/peptideprophet | SCR_000274 | 2026-02-14 01:59:41 | 4 | |||||||
|
pvac Resource Report Resource Website |
pvac (RRID:SCR_000359) | pvac | software resource | Software package that contains the function for filtering genes by the proportion of variation accounted for by the first principal component (PVAC). | microarray, one channel, quality control, affymetrix, principal component analysis, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | biotools:pvac, OMICS_02031 | https://bio.tools/pvac | SCR_000359 | pvac: PCA-based gene filtering for Affymetrix arrays | 2026-02-14 01:59:41 | 0 | ||||||
|
Flicker Resource Report Resource Website |
Flicker (RRID:SCR_000288) | software resource | An open-source stand-alone computer program for visually comparing 2D gel images. | mac os x, unix/linux, windows, java, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:10027264 | Free, Available for download, Freely available | OMICS_02538, biotools:nci_flicker | https://bio.tools/nci_flicker | SCR_000288 | 2026-02-14 01:59:41 | 0 | |||||||
|
MeQA Resource Report Resource Website |
MeQA (RRID:SCR_000317) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 31, 2022. Software for pre-processing, quality assessment, read distribution and methylation estimation for MeDIP-sequence datasets. It has the ability to quickly analyze sequence data for DNA methylation. This software integrates customized scripting and existing utilities tools that work on both paired end and single end data. | quality assessment, read distribution, methylation estimation, medip, medip-sequence, dna methylation, utilities tool, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Tongji University; Shanghai; China |
PMID:22199384 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:meqa, OMICS_00616 | https://bio.tools/meqa | SCR_000317 | 2026-02-14 01:59:41 | 0 | |||||||
|
Micro-Analyzer Resource Report Resource Website |
Micro-Analyzer (RRID:SCR_000394) | Micro-Analyzer | software resource | Java tool that performs the preprocessing of Expression and SNPs microarray Affymetrix. The software allows the automatic download and the use of the clustering and visualization software as the Mev 4.0. The tool is equipped by a graphical interface (Swing) that allows to the user to: Create the workspace (files .cel, preferred algorithms , output, libraries to use); Run/save analysis and workspace settings (xml); Efficient download of the libraries (http, ftp, MD5); Customize basic and graphical settings (objects serialization and deserialization). Type of SNPs: Mapping 500k or preceding chips, SNP 5.0, SNP 6.0. Available for 32 or 64 bit systems, and for Windows and Linux Systems. | windows, linux, java, java swing, gene expression, snp, microarray, affymetrix, preprocessing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23731720 | Free, Available for download, Freely available | OMICS_01919, biotools:microanalyzer | https://bio.tools/microanalyzer | SCR_000394 | microAnalyzer | 2026-02-14 01:59:43 | 0 | |||||
|
SAMBLASTER Resource Report Resource Website 10+ mentions |
SAMBLASTER (RRID:SCR_000468) | software resource | Software tool to mark duplicates and extract discordant and split reads from SAM files. This fast and flexible program for marking duplicates in read-id grouped paired-end SAM files can also optionally output discordant read pairs and/or split read mappings to separate SAM files, and/or unmapped/clipped reads to a separate FASTQ file. When marking duplicates, samblaster will require approximately 20MB of memory per 1M read pairs. | standalone software, c++, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Virginia; Virginia; USA |
PMID:24812344 DOI:10.1093/bioinformatics/btu314 |
Free, Available for download, Freely available | biotools:samblaster, OMICS_04682 | https://bio.tools/samblaster https://sources.debian.org/src/samblaster/ |
SCR_000468 | 2026-02-14 01:59:46 | 18 | |||||||
|
TAPyR Resource Report Resource Website 1+ mentions |
TAPyR (RRID:SCR_000588) | software resource | An efficient software tool for the local alignment of pyrosequencing reads produced by the GS FLX (454) Genome Analyzer technology against a reference genome sequence. The approach explores the characteristics of the data in re-sequencing applications and uses state of the art BWT-based indexing techniques combined with a flexible seed-based approach, leading to a fast and accurate algorithm which needs very little user parameterization. Although initially developed having this specific technology in mind, this software performs equally well on any other platform that can return its sequencing reads in the FASTA, FASTQ or SFF formats, including Illumina, Ion Torrent and Pacific Biosciences technologies. | gs flx, genome analyzer, bwt, fasta, fastq, sff formats, pyrosequencing reads, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:21672185 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:tapyr, OMICS_00693 | https://bio.tools/tapyr | SCR_000588 | Tool for Alignment of Pyrosequencing Reads | 2026-02-14 01:59:46 | 1 | ||||||
|
MuTect Resource Report Resource Website 50+ mentions |
MuTect (RRID:SCR_000559) | MuTect | software resource | Software for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes. | next-generation sequencing, somatic mutation, tumor, normal, genome, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Broad Institute |
Cancer | PMID:23396013 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:mutect, OMICS_00087 | https://bio.tools/mutect | SCR_000559 | Mutect | 2026-02-14 01:59:45 | 91 | ||||
|
SRMA Resource Report Resource Website |
SRMA (RRID:SCR_000669) | SRMA | software resource | A post-alignment micro re-aligner for next-generation high throughput sequencing data. | matlab, sequence re-alignment, command-line, java, next generation sequencing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20932289 | Free, Available for download, Freely available | biotools:srma, OMICS_01079 | https://bio.tools/srma | SCR_000669 | Short Read Micro re-Aligner | 2026-02-14 01:59:47 | 0 | |||||
|
AffyRNADegradation Resource Report Resource Website |
AffyRNADegradation (RRID:SCR_000118) | AffyRNADegradation | software resource | Software package that helps with the assessment and correction of RNA degradation effects in Affymetrix 3' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation. | rna degradation, gene expression, microarray, preprocessing, affymetrix, rna, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor has parent organization: University of Leipzig; Saxony; Germany |
PMID:23097420 | Free, Available for download, Freely available | OMICS_01975, biotools:affyrnadegradation | https://bio.tools/affyrnadegradation | SCR_000118 | 2026-02-14 01:59:37 | 0 | ||||||
|
SOAPfusion Resource Report Resource Website 1+ mentions |
SOAPfusion (RRID:SCR_000079) | SOAPfusion | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 22,2022. An open source software tool for fusion discovery with paired-end RNA-Seq reads. The tool follows a different strategy by finding fusions directly and verifying them, differentiating it from all other existing tools by finding the candidate regions and searching for the fusions afterwards. | software, open source, free, RNA, sequencing, data, computing, research, analysis, rna-seq, candidate regions, bio.tools |
is listed by: OMICtools is listed by: SOAP is listed by: bio.tools is listed by: Debian |
Guangdong Innovative Research Team Program ; General Research Fund of the Hong Kong Government |
PMID:24123671 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01358, biotools:soapfusion | https://bio.tools/soapfusion | SCR_000079 | 2026-02-14 01:59:36 | 3 | |||||
|
timecourse Resource Report Resource Website 1+ mentions |
timecourse (RRID:SCR_000077) | timecourse | software resource | Software functions for data analysis and graphical displays for developmental microarray time course data. | microarray, differential expression, time course, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: CRAN has parent organization: Bioconductor has parent organization: University of California at Berkeley; Berkeley; USA |
Free, Available for download, Freely available | OMICS_01980, biotools:timecourse | https://bio.tools/timecourse | SCR_000077 | timecourse - Statistical Analysis for Developmental Microarray Time Course Data | 2026-02-14 01:59:36 | 5 | ||||||
|
Patchwork Resource Report Resource Website 1+ mentions |
Patchwork (RRID:SCR_000072) | Patchwork | software resource | Software tool for analyzing and visualizing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. The data input is in the format of whole-genome sequencing data which enables characterization of genomic alterations ranging in size from point mutations to entire chromosomes. High quality results are obtained even if samples have low coverage, ~4x, low tumor cell content or are aneuploid. Patchwork takes BAM files as input whereas PatchworkCG takes input from CompleteGenomics files. TAPS performs the same analysis as Patchwork but for microarray data. | genome, allele, copy number, bam, unix, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Uppsala University; Uppsala; Sweden |
Cancer, Tumor | PMID:23531354 | Free, Available for download, Freely available | biotools:patchwork, OMICS_02118 | https://bio.tools/patchwork | SCR_000072 | 2026-02-14 01:59:36 | 9 | |||||
|
SNAVI Resource Report Resource Website |
SNAVI (RRID:SCR_000091) | software resource | Desktop application for analysis and visualization of large-scale cell signaling networks. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
PMID:19154595 | Free, Available for download, Freely available | biotools:snavi, OMICS_04122 | https://bio.tools/snavi | SCR_000091 | Signaling Networks Analysis and Visualization | 2026-02-14 01:59:37 | 0 | ||||||
|
Phenoscape Resource Report Resource Website 1+ mentions |
Phenoscape (RRID:SCR_003799) | Phenoscape | data or information resource, portal | Project to create a scalable infrastructure that enables linking phenotypes across different fields of biology by the semantic similarity of their descriptions. | phenotype, bio.tools |
is listed by: Debian is listed by: bio.tools is parent organization of: Teleost Anatomy Ontology is parent organization of: Vertebrate Taxonomy Ontology is parent organization of: Phenoscape Knowledgebase |
NSF DBI-1062404; NSF DBI-1062542; NSF BDI-0641025; NSF EF-0905606; NSF EF-0423641 |
biotools:Phenoscape, nlx_158096 | https://bio.tools/Phenoscape | SCR_003799 | 2026-02-14 02:05:03 | 8 |
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