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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Oncodrive-fm Resource Report Resource Website 10+ mentions |
Oncodrive-fm (RRID:SCR_010781) | Oncodrive-fm | software resource | An approach to uncover driver genes or gene modules. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00157, biotools:oncodrivefm | https://bio.tools/oncodrivefm | SCR_010781 | 2026-02-14 02:02:05 | 14 | ||||||||
|
SSAKE Resource Report Resource Website 10+ mentions |
SSAKE (RRID:SCR_010753) | SSAKE | software resource | Software designed to help leverage the information from short sequences reads by stringently clustering them into contigs that can be used to characterize novel sequencing targets. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:10.1093/bioinformatics/btl629 | biotools:ssake, OMICS_00033 | https://bio.tools/ssake https://sources.debian.org/src/ssake/ |
SCR_010753 | 2026-02-14 02:02:03 | 11 | |||||||
|
CopySeq Resource Report Resource Website 1+ mentions |
CopySeq (RRID:SCR_010758) | CopySeq | software resource | A computational tool that analyzes the depth-of-coverage of high-throughput DNA sequencing reads, and can integrate paired-end and breakpoint junction analysis based CNV-analysis approaches, to infer locus copy-number genotypes. | java, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: European Molecular Biology Laboratory |
PMID:21085617 | biotools:copyseq, OMICS_00055 | https://bio.tools/copyseq | SCR_010758 | 2026-02-14 02:01:49 | 1 | |||||||
|
FreeBayes Resource Report Resource Website 1000+ mentions |
FreeBayes (RRID:SCR_010761) | FreeBayes | software resource | A Bayesian genetic variant detector designed to find small polymorphisms, specifically SNPs, indels, MNPs, and complex events smaller than the length of a short-read sequencing alignment. | single-nucleotide polymorphism, indel, insertion, deletion, multi-nucleotide polymorphism, complex event, composite insertion, substitution event, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
DOI:arXiv:1207.3907 | OMICS_00059, biotools:freebayes | https://bio.tools/freebayes https://sources.debian.org/src/freebayes/ |
SCR_010761 | 2026-02-14 02:02:03 | 1982 | |||||||
|
MICSA Resource Report Resource Website |
MICSA (RRID:SCR_010860) | MICSA | software resource | A software package for the identification of transcription factor binding sites in ChIP-Seq data, developed by Computational Systems Biology of Cancer group at the Bioinformatics Laboratory of Institut Curie (Paris). | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Curie Institute; Paris; France |
biotools:micsa, OMICS_00447 | https://bio.tools/micsa | SCR_010860 | MICSA: Motif Identification for ChIP-Seq Analysis, Motif Identification for ChIP-Seq Analysis | 2026-02-14 02:02:06 | 0 | |||||||
|
NOrMAL Resource Report Resource Website 50+ mentions |
NOrMAL (RRID:SCR_010889) | NOrMAL | software resource | A command line software tool for accurate placing of the nucleosomes using a Modified Gaussian Mixture Model. It was designed to resolve overlapping nucleosomes and extract extra information (fuzziness, probability, etc.) of nucleosome placement. To achieve this goal the tool clusters the input tags according to Nucleosome Model (see the paper for detailed description) using EM learning process. The tool is written in C++. There are no special requirements except for g++ compiler and *nix environment to compile and use the tool. It was checked to compile using g++ compiler under Ubuntu 11.04 and Mac OS X 10.6 | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at Riverside; California; USA |
Free for academic use | OMICS_00504, biotools:normal | https://bio.tools/normal | SCR_010889 | NOrMAL: Accurate Nucleosome Positioning using a Modified Gaussian Mixture Model | 2026-02-14 02:02:06 | 83 | ||||||
|
Asterias Resource Report Resource Website 1+ mentions |
Asterias (RRID:SCR_010936) | Asterias | software resource | A set of web-based applications for the analysis of genomic and proteomic data. Asterias combines Python with R and C/C++, using MPI for parallelization, and aspires to become a standard for high-performance, distributed, web-based bioinformatics and biostatistics applications. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Spanish National Cancer Research Center |
PMID:17488846 | Public | OMICS_00747, biotools:asterias | https://bio.tools/asterias | SCR_010936 | 2026-02-14 02:02:07 | 1 | ||||||
|
Chipster Resource Report Resource Website 50+ mentions |
Chipster (RRID:SCR_010939) | Chipster | software resource | A user-friendly analysis software for high-throughput data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00751, biotools:chipster | https://bio.tools/chipster | SCR_010939 | 2026-02-14 02:01:52 | 81 | ||||||||
|
MethMarker Resource Report Resource Website 1+ mentions |
MethMarker (RRID:SCR_010908) | MethMarker | software resource | Tool that facilitates the design and optimization of gene-specific DNA methylation assays. Beyond its use as an epigenetic primer-design tool, it provides extensive support for epigenetic biomarker optimization. Download MethMarker or start it directly from within your web browser. | dna methylation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Max-Planck-Institute for Informatics; Saarbrucken; Germany |
PMID:19804638 | Acknowledgement requested | OMICS_00636, biotools:methmarker | https://bio.tools/methmarker | SCR_010908 | 2026-02-14 02:02:07 | 2 | ||||||
|
SISSRs Resource Report Resource Website 10+ mentions |
SISSRs (RRID:SCR_010866) | SISSRs | software resource | Anl algorithm for precise identification of binding sites from short reads generated from ChIP-Seq experiments. | perl, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:18684996 PMID:22130889 |
biotools:sissrs, OMICS_00463 | https://bio.tools/sissrs | SCR_010866 | Site Identification from Short Sequence Reads | 2026-02-14 02:02:05 | 16 | ||||||
|
ZINBA Resource Report Resource Website 10+ mentions |
ZINBA (RRID:SCR_010868) | ZINBA | software resource | Software to identify genomic regions enriched in a variety of ChIP-seq and related next-generation sequencing experiments (DNA-seq), calling both broad and narrow modes of enrichment across a range of signal-to-noise ratios. ZINBA models and accounts for factors that co-vary with background or experimental signal, such as G/C content, and identifies enrichment in genomes with complex local copy number variations. ZINBA provides a single unified framework for analyzing DNA-seq experiments in challenging genomic contexts. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
PMID:21787385 | GNU General Public License, v3 | biotools:zinba, OMICS_00465 | https://bio.tools/zinba | SCR_010868 | zinba - Zero Inflated Negative Binomial Algorithm, Zero Inflated Negative Binomial Algorithm | 2026-02-14 02:02:06 | 13 | |||||
|
Aroma.affymetrix Resource Report Resource Website 10+ mentions |
Aroma.affymetrix (RRID:SCR_010919) | Aroma.affymetrix | software resource | An R package for analyzing large Affymetrix data sets. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00703, biotools:aroma.affymetrix | https://bio.tools/aroma.affymetrix | SCR_010919 | 2026-02-14 02:02:06 | 32 | ||||||||
|
Eddy Lab Software Resource Report Resource Website 10+ mentions |
Eddy Lab Software (RRID:SCR_001458) | software resource | Software library containing tools for statistical manipulations of data. Tools include profile hidden Markov models for biological sequence analysis, RNA structure analysis, and a prototype noncoding RNA genefinder. | software repository, statistics, data, statistical analysis, statistical manipulation, markov model, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Janelia Research has parent organization: Howard Hughes Medical Institute |
Free, Available for download, Freely available | nif-0000-08778, biotools:pknots | https://bio.tools/pknots | http://selab.janelia.org/software.html | SCR_001458 | Eddy Lab: Software, Eddy Lab - Software | 2026-02-14 02:00:04 | 21 | ||||||
|
PyLOH Resource Report Resource Website 1+ mentions |
PyLOH (RRID:SCR_001511) | software resource | Software for deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity. The model resolves the identifiability problem by integrating two types of sequencing information - somatic copy number alterations and loss of heterozygosity - within an unified probabilistic framework. | standalone software, python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24695406 | Free, Available for download, Freely available | OMICS_03559, biotools:pyloh | https://bio.tools/pyloh | SCR_001511 | 2026-02-14 02:00:04 | 4 | |||||||
|
TANGO Resource Report Resource Website 100+ mentions |
TANGO (RRID:SCR_001770) | TANGO | software resource | A computer algorithm to predict aggregation nucleating regions in proteins as well the effect of mutations and environmental conditions on the aggregation propensity of these regions. | polypeptide chain, polypeptide, peptide, protein, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Center for Genomic Regulation; Barcelona; Spain |
PMID:15361882 | Free, Freely available | biotools:tango, OMICS_03859 | https://bio.tools/tango | SCR_001770 | 2026-02-14 02:00:17 | 114 | ||||||
|
Cuffdiff Resource Report Resource Website 1000+ mentions |
Cuffdiff (RRID:SCR_001647) | Cuffdiff | software resource | Software that estimates expression at transcript-level resolution and controls for variability evident across replicate libraries. | differential expression, rna-seq, transcript, splicing, promoter, coding sequence, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Cufflinks has parent organization: University of Maryland; Maryland; USA |
PMID:23222703 | Free, Available for download, Freely available | biotools:cuffdiff, OMICS_01969 | https://bio.tools/cuffdiff | SCR_001647 | Cuffdiff 2 | 2026-02-14 02:00:05 | 3832 | |||||
|
PennSeq Resource Report Resource Website 1+ mentions |
PennSeq (RRID:SCR_001763) | PennSeq | software resource | Software for isoform-specific gene expression quantification in RNA-Seq by modeling non-uniform read distribution. Instead of making parametric assumptions, they give adequate weight to the underlying data by the use of a non-parametric approach. The rationale is that regardless what factors lead to non-uniformity, whether it is due to hexamer priming bias, local sequence bias, positional bias, RNA degradation, mapping bias or other unknown reasons, the probability that a fragment is sampled from a particular region will be reflected in the aligned data. This empirical approach thus maximally reflects the true underlying non-uniform read distribution. | isoform, gene expression, rna-seq, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24362841 | Free, Available for download, Freely available | biotools:pennseq, OMICS_01946 | https://bio.tools/pennseq | SCR_001763 | 2026-02-14 02:00:10 | 4 | ||||||
|
PhosphoSitePlus: Protein Modification Site Resource Report Resource Website 500+ mentions |
PhosphoSitePlus: Protein Modification Site (RRID:SCR_001837) | PSP | knowledge environment resource, data or information resource, portal | A freely accessible on-line systems biology resource devoted to all aspects of protein modification, as well as other post-translational modifications. It provides valuable and unique tools for both cell biologists and mass spectroscopists. PhosphoSite is a human- and mouse-centric database. It includes features such as: viewing the locations of modified residues on molecular models; browsing and searching MS2 records by disease, tissue, and cell line; submitting lists of peptides to identify previously reported genes; searching by sub-cellular localization, treatment, tissues, cell types, cell lines and diseases, and protein types and protein domains; searching for experimentally-verified kinase substrates and viewing preferred substrate motifs; and viewing MS2 spectra for peptides and sites not previously published. | portal, mass spectroscopist, molecular model, mouse, post translational, subcellular localization, protein modification, post-translational modification, protein phosphorylation, protein structure, protein function, ubiquitinylation, acetylation, cellular component, cell type, visualization, data repository, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian is related to: Cytoscape is related to: ConsensusPathDB has parent organization: Cell Signaling Technology |
NCI ; NIAAA R44 AA014848; NIGMS R43 GM65768 |
PMID:22135298 | Free, Freely available | biotools:phosphositeplus, nif-0000-10399 | https://bio.tools/phosphositeplus | SCR_001837 | PhosphoSitePlus, PhosphoSite | 2026-02-14 02:00:09 | 903 | ||||
|
R Project for Statistical Computing Resource Report Resource Website 10000+ mentions |
R Project for Statistical Computing (RRID:SCR_001905) | R | software resource | Software environment and programming language for statistical computing and graphics. R is integrated suite of software facilities for data manipulation, calculation and graphical display. Can be extended via packages. Some packages are supplied with the R distribution and more are available through CRAN family.It compiles and runs on wide variety of UNIX platforms, Windows and MacOS. | R software, statistical, computing, graphics, programming, language, bio.tools |
is used by: UTR is used by: MSstats is used by: CummeRbund is used by: deFuse is used by: JASP is used by: Boruta is used by: NMRProcFlow is used by: PlotsOfData is used by: rtransparent is used by: shinyCircoss is listed by: OMICtools is listed by: bio.tools is listed by: Debian is affiliated with: CRAN is affiliated with: factoextra is affiliated with: dendsort is affiliated with: viridis is affiliated with: RColorBrewer is affiliated with: statmod is related to: Sweave is related to: rOpenSci is related to: R Manuals is related to: Bioconductor is related to: ggplot2 is related to: madsim is related to: Solas is related to: braincog is related to: clustree is related to: PhenoSpD is related to: geomorph is related to: NeuroAnatomy Toolbox is related to: dplyr is related to: glmmADMB is related to: clusterProfiler is related to: ropls is related to: mixOmics is related to: FlowSOM is related to: Rtsne is related to: scran is related to: Rsubread is related to: riboSeqR is related to: Biostrings is related to: riboWaltz is related to: GenomicFeatures is related to: devtools is related to: affy is related to: affydata is related to: Heatmapper is related to: toxprofileR is related to: LTRpred is related to: RaceID is related to: PRSice is related to: Genomic Ranges is related to: Goseq is related to: GAGE is related to: metagear is related to: pagoda2 is related to: dndSCV is related to: tidyr is related to: ClustVis is related to: IDR is related to: NeuroAnatomy Toolbox is related to: rjags is related to: gProfiler2 is related to: knitr is related to: EpiEstim is related to: Minimum-Hypergeometric Test is related to: Network-Based R-Statistics is related to: seqpac is related to: survminer is related to: Vector Generalized Linear and Additive Models is related to: LEA is related to: StAMPP is related to: Betareg is related to: Harrell Miscellaneous is related to: simplePHENOTYPES is related to: Bayesian Generalized Linear Regression is related to: ranger is related to: h2o4gpu is related to: ridge regression Best Linear Unbiased Prediction is related to: Classification And Regression Training is related to: Rphenograph is related to: Peptides is related to: taxize is related to: seqinr is related to: reshape2 is related to: monaLisa is related to: mia is related to: Rtsne is related to: R package:stats-package is related to: R package: maxstat is related to: stats |
PMID:18252159 | SCR_021974, nif-0000-10474, OMICS_01147, biotools:r | https://cran.r-project.org/src/base/R-3/ https://bio.tools/r |
SCR_001905 | R software, The R Project for Statistical Computing, R project, R Project, R, R version 3.5.1, R Package, R-3, R version 3.6.1, R Project for Statistical Computing | 2026-02-14 02:00:20 | 47818 | ||||||
|
Pecan Resource Report Resource Website 50+ mentions |
Pecan (RRID:SCR_001909) | software resource | A Java consistency based multiple sequence alignment software program. | java, sequence, alignment, consistency, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of California at Santa Cruz; California; USA |
PMID:18849524 | Free, Available for download, Freely available | OMICS_03739, biotools:pecan | http://hgwdev.cse.ucsc.edu/~benedict/code/Pecan.html https://bio.tools/pecan |
SCR_001909 | 2026-02-14 02:00:14 | 50 |
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