Searching the RRID Resource Information Network
Are you sure you want to leave this community? Leaving the community will revoke any permissions you have been granted in this community.
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.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
SAMStat Resource Report Resource Website 10+ mentions |
SAMStat (RRID:SCR_005432) | SAMStat | software resource | C software program for displaying sequence statistics for next generation sequencing. Works with large fasta, fastq and SAM/BAM files. | sequence statistic, c, next generation sequencing, fasta file, fastq file, sam file, bam file, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: RIKEN Yokohama Institute; Kanagawa; Japan |
PMID:21088025 | Acknowledgement requested | biotools:samstat, OMICS_01073 | https://bio.tools/samstat | SCR_005432 | 2026-02-14 02:00:53 | 38 | ||||||
|
MethylViewer Resource Report Resource Website 1+ mentions |
MethylViewer (RRID:SCR_005448) | MethylViewer | software resource | A simple integrated software tool for handling MAP (methyltransferase accessibility protocol) and MAP-IT (MAP individual templates) footprinting projects. It can process sequence data (*.txt, *.ab1 and *.scf) derived from the use of up to four different DNA methyltransferases. | primer design, bisulfite sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Leeds; West Yorkshire; United Kingdom |
PMID:20959287 | OMICS_00608, biotools:methylviewer | https://bio.tools/methylviewer | SCR_005448 | 2026-02-14 02:00:55 | 2 | |||||||
|
Bis-SNP Resource Report Resource Website 50+ mentions |
Bis-SNP (RRID:SCR_005439) | Bis-SNP | software resource | A software package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping and accurate DNA methylation calling in bisulfite treated massively parallel sequencing (Bisulfite-seq, NOMe-seq, RRBS and any other bisulfite treated sequencing) with Illumina directional library protocol. It contains the following key features: * Call and summarize methylation of any cytosine context provided (CpG, CHH, CHG, GCH et.al.); * Work for single end and paired-end data; * Accurtae variant detection. Enable base quality recalibration and indel calling in bisulfite sequencing; * Based on Java map-reduce framework, allow multi-thread computing. Cross-platform; * Allow multiple output format, detailed VCF files, CpG haplotype reads file for mono-allelic methylation analysis, simplified bedGraph, wig and bed format for visualization in UCSC genome broswer and IGV browser. BisSNP uses bayesian inference with locus specific methylation probabilities and bisulfite conversion rate of different cytosine context(not only CpG, CHH, CHG in Bisulfite-seq, but also GCH et.al. in other bisulfite treated sequencing) to determine genotypes and methylation levels simultaneously., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Southern California; Los Angeles; USA |
PMID:22784381 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:bis-snp, OMICS_00591 | https://bio.tools/bis-snp | SCR_005439 | Bis-SNP - A bisulfite space genotyper & methylation caller, Bis-SNP - A bisulfite space genotyper and methylation caller | 2026-02-14 02:00:54 | 50 | |||||
|
DistMap Resource Report Resource Website 10+ mentions |
DistMap (RRID:SCR_005473) | DistMap | software resource | A user-friendly software pipeline designed to map short reads in a MapReduce framework on a local Hadoop cluster. It is designed to be easily implemented by researchers who do not have expert knowledge of bioinformatics. As it does not have any dependencies, it provides full flexibility and control to the user. The user can use any version of a compatible mapper and any reference genome assembly. There is no need to maintain the mapper, reference or DistMap source code on each of the slaves (nodes) in the Hadoop cluster, making maintenance extremely easy. | mapreduce/hadoop, command line, hadoop cluster, next-generation sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Veterinary Medicine Vienna; Vienna; Austria has parent organization: Google Code |
PMID:24009693 | GNU General Public License, v3 | OMICS_00660, biotools:distmap | https://bio.tools/distmap | SCR_005473 | 2026-02-14 02:01:06 | 23 | ||||||
|
Stampy Resource Report Resource Website 100+ mentions |
Stampy (RRID:SCR_005504) | Stampy | software resource | A software package for the mapping of short reads from illumina sequencing machines onto a reference genome. It''s recommended for most workflows, including those for genomic resequencing, RNA-Seq and Chip-seq. Stampy excels in the mapping of reads containing that contain sequence variation relative to the reference, in particular for those containing insertions or deletions. It can map reads from a highly divergent species to a reference genome for instance. Stampy achieves high sensitivity and speed by using a fast hashing algorithm and a detailed statistical model. Stampy has the following features: * Maps single, paired-end and mate pair Illumina reads to a reference genome * Fast: about 20 Gbase per hour in hybrid mode (using BWA) * Low memory footprint: 2.7 Gb shared memory for a 3Gbase genome * High sensitivity for indels and divergent reads, up to 10-15% * Low mapping bias for reads with SNPs * Well calibrated mapping quality scores * Input: Fastq and Fasta; gzipped or plain * Output: SAM, Maq''s map file * Optionally calculates per-base alignment posteriors * Optionally processes part of the input * Handles reads of up to 4500 bases | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Wellcome Trust Centre for Human Genetics |
PMID:20980556 | OMICS_00691, biotools:stampy | https://bio.tools/stampy | SCR_005504 | 2026-02-14 02:01:07 | 182 | |||||||
|
NGSView Resource Report Resource Website 1+ mentions |
NGSView (RRID:SCR_005637) | NGSView | software resource | A generally applicable, flexible and extensible next-generation sequence alignment editor. The software allows for visualization and manipulation of millions of sequences simultaneously on a desktop computer, through a graphical interface. | next-generation sequence, alignment, edit, visualization, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
Acknowledgement requested | biotools:ngsview, OMICS_00891 | https://bio.tools/ngsview | SCR_005637 | 2026-02-14 02:00:58 | 2 | |||||||
|
HiCUP Resource Report Resource Website 100+ mentions |
HiCUP (RRID:SCR_005569) | HiCUP | software resource | A tool for mapping and performing quality control on Hi-C data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Babraham Institute |
OMICS_00523, biotools:hicup | https://bio.tools/hicup | SCR_005569 | Hi-C User Pipeline | 2026-02-14 02:01:09 | 273 | |||||||
|
RUM Resource Report Resource Website 1+ mentions |
RUM (RRID:SCR_008818) | RUM | software resource | An alignment, junction calling, and feature quantification pipeline specifically designed for Illumina RNA-Seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
OMICS_01249, biotools:rum | https://bio.tools/rum https://github.com/itmat/rum/wiki |
SCR_008818 | Rna seq Unified Mapper | 2026-02-14 02:01:48 | 7 | |||||||
|
QuasiRecomb Resource Report Resource Website 10+ mentions |
QuasiRecomb (RRID:SCR_008812) | QuasiRecomb | software resource | A jumping hidden Markov model that describes the generation of the viral quasispecies and a method to infer its parameters by analysing next generation sequencing data. | haplotype, next-generation sequencing, virus, parameter, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23383997 | OMICS_00229, biotools:quasirecomb | https://bio.tools/quasirecomb | SCR_008812 | QuasiRecomb - Probabilistic inference of viral Quasispecies | 2026-02-14 02:01:45 | 32 | ||||||
|
XPN Resource Report Resource Website 1+ mentions |
XPN (RRID:SCR_008845) | XPN | software resource | Merging Two Gene Expression Studies via Cross Platform Normalization. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
OMICS_00863, biotools:xpn | https://bio.tools/xpn | SCR_008845 | 2026-02-14 02:01:48 | 2 | ||||||||
|
MuSiC Resource Report Resource Website 100+ mentions |
MuSiC (RRID:SCR_008792) | MuSiC | software resource | A set of tools aimed at determining the significance of somatic mutations discovered within a given cohort of cancer samples, incorporating the cohort''s alignment data, variant lists and any relevant clinical data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Washington University in St. Louis; Missouri; USA |
PMID:22759861 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:MuSiC2, OMICS_00152 | https://bio.tools/MuSiC2 https://github.com/ding-lab/MuSiC2/blob/master/README.md |
SCR_008792 | Mutational Significance In Cancer | 2026-02-14 02:01:45 | 485 | |||||
|
GEMINI Resource Report Resource Website 500+ mentions |
GEMINI (RRID:SCR_014819) | software resource | Framework for exploring genetic variation in the context of the genome annotations available for the human genome. Users can load a VCF file into a database and each variant is automatically annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks, OMIM, dbSNP, KEGG, and HPRD. | framework, genetic variation, annotation, human, genome, vcf, database, , bio.tools, FASEB list |
uses: KEGG uses: ENCODE uses: OMIM uses: dbSNP uses: HPRD - Human Protein Reference Database is listed by: Debian is listed by: bio.tools has parent organization: University of Utah; Utah; USA |
DOI:10.1371/journal.pcbi.1003153 | Freely available | biotools:gemini | https://github.com/arq5x/gemini https://bio.tools/gemini |
SCR_014819 | GEnome MINIng (GEMINI), GEMINI - a flexible framework for exploring genome variation, Genome Mining, GEnome MINIng | 2026-02-14 02:03:02 | 515 | ||||||
|
eDMR Resource Report Resource Website 10+ mentions |
eDMR (RRID:SCR_006960) | eDMR | software resource | Comprehensive differentially methylated regions (DMR) analysis based on bimodal normal distribution model and weighted cost function for regional methylation analysis optimization. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
MIT License | biotools:edmr, OMICS_00622 | https://bio.tools/edmr | SCR_006960 | 2026-02-14 02:01:26 | 19 | |||||||
|
Peakzilla Resource Report Resource Website 1+ mentions |
Peakzilla (RRID:SCR_007471) | Peakzilla | software resource | An algorithm to identify transcription factor binding sites from ChIP-seq data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
biotools:peakzilla, OMICS_00454 | https://bio.tools/peakzilla | SCR_007471 | 2026-02-14 02:01:33 | 6 | ||||||||
|
AmpliconNoise Resource Report Resource Website 50+ mentions |
AmpliconNoise (RRID:SCR_007814) | AmpliconNoise | software resource | A collection of programs for the removal of noise from 454 sequenced PCR amplicons. This project also includes the Perseus algorithm for chimera removal. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
DOI:10.1186/1471-2105-12-38 | biotools:pyronoise, OMICS_01112 | https://bio.tools/pyronoise https://sources.debian.org/src/anfo/ |
SCR_007814 | 2026-02-14 02:01:30 | 90 | |||||||
|
Kalign Resource Report Resource Website 100+ mentions |
Kalign (RRID:SCR_011810) | Kalign | software resource | A fast and accurate multiple sequence alignment algorithm. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: European Bioinformatics Institute |
PMID:16343337 DOI:10.1093/bioinformatics/btz795 |
Free | OMICS_00978, biotools:kalign | https://bio.tools/kalign https://sources.debian.org/src/kalign/ |
SCR_011810 | 2026-02-14 02:02:27 | 119 | ||||||
|
CGView Resource Report Resource Website 100+ mentions |
CGView (RRID:SCR_011779) | CGView | software resource | A Java package for generating high quality, zoomable maps of circular genomes. Its primary purpose is to serve as a component of sequence annotation pipelines, as a means of generating visual output suitable for the web., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: University of Alberta; Alberta; Canada |
DOI:10.1093/bioinformatics/bti054 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00905, biotools:cgview | https://bio.tools/cgview https://sources.debian.org/src/cgview/ |
SCR_011779 | Circular Genome Viewer | 2026-02-14 02:02:04 | 304 | |||||
|
PSAR-Align Resource Report Resource Website 1+ mentions |
PSAR-Align (RRID:SCR_011814) | PSAR-Align | software resource | Software for improving multiple sequence alignment using probabilistic sampling. | c++, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24222208 | Free | OMICS_00987, biotools:psar | https://bio.tools/psar | SCR_011814 | PSAR-Align: improving multiple sequence alignment using probabilistic sampling | 2026-02-14 02:02:28 | 1 | |||||
|
Gaggle Resource Report Resource Website |
Gaggle (RRID:SCR_011780) | Gaggle | software resource | An open source software tool for visualizing high-density data plotted against coordinates on the genome. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Open unspecified license, Free | biotools:ggb, OMICS_00909 | https://bio.tools/ggb | SCR_011780 | 2026-02-14 02:02:26 | 0 | |||||||
|
PatMaN Resource Report Resource Website 50+ mentions |
PatMaN (RRID:SCR_011821) | PatMaN | software resource | Software that searches for short patterns in large DNA databases, allowing for approximate matches., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | c++, bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:18467344 DOI:10.1093/bioinformatics/btn223 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00997, biotools:patman | https://bio.tools/patman https://sources.debian.org/src/patman/ |
SCR_011821 | PatMaN - A DNA pattern matcher for short sequences | 2026-02-14 02:02:28 | 61 |
Can't find your Tool?
We recommend that you click next to the search bar to check some helpful tips on searches and refine your search firstly. Alternatively, please register your tool with the SciCrunch Registry by adding a little information to a web form, logging in will enable users to create a provisional RRID, but it not required to submit.
Welcome to the NIF Resources search. From here you can search through a compilation of resources used by NIF and see how data is organized within our community.
You are currently on the Community Resources tab looking through categories and sources that NIF has compiled. You can navigate through those categories from here or change to a different tab to execute your search through. Each tab gives a different perspective on data.
If you have an account on NIF then you can log in from here to get additional features in NIF such as Collections, Saved Searches, and managing Resources.
Here is the search term that is being executed, you can type in anything you want to search for. Some tips to help searching:
If you are logged into NIF you can add data records to your collections to create custom spreadsheets across multiple sources of data.
Here are the facets that you can filter the data by.
If you have any further questions please check out our FAQs Page to ask questions and see our tutorials. Click this button to view this tutorial again.
Welcome to the Neuroscience Information Framework Project, designed to serve the biomedical research community. NIF maintains the largest searchable collection of neuroscience data, the largest catalog of biomedical resources, and the largest ontology for neuroscience on the web. We welcome all feedback and suggestions and are actively looking for resource providers to make their resources accessible through NIF. Learn about the tools available to help you share your data and discover a dynamic inventory of Web-based neuroscience resources.
