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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
LIMMA Resource Report Resource Website 10000+ mentions |
LIMMA (RRID:SCR_010943) | LIMMA | data analysis software, software resource, data processing software, software application | Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression. | analysis, gene, expression, microarray, data, linear, model, bio.tools |
is used by: Glimma is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: GEO2R is related to: Bioconductor |
Free, Available for download, Freely available | biotools:limma, OMICS_00769 | https://omictools.com/limma-tool https://bio.tools/limma https://sources.debian.org/src/r-bioc-limma/ |
SCR_010943 | Linear Models for Microarray Data | 2026-02-14 02:02:08 | 24583 | ||||||
|
NPS Resource Report Resource Website 100+ mentions |
NPS (RRID:SCR_010890) | NPS | software resource | A python software package that can identify nucleosome positions given histone-modification ChIP-seq or nucleosome sequencing at the nucleosome level. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: iNPS has parent organization: Dana-Farber Cancer Institute |
PMID:19014516 | OMICS_00505, biotools:nps | https://bio.tools/nps | SCR_010890 | Nucleosome Positioning from Sequencing, NPS (Nucleosome Positioning from Sequencing) | 2026-02-14 02:02:07 | 121 | ||||||
|
BRB-ArrayTools Resource Report Resource Website 500+ mentions |
BRB-ArrayTools (RRID:SCR_010938) | BRB-ArrayTools | software resource | An integrated software package for the visualization and statistical analysis of DNA microarray gene expression data., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: National Cancer Institute |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00750, biotools:brb-arraytools | https://bio.tools/brb-arraytools | SCR_010938 | 2026-02-14 02:02:08 | 569 | |||||||
|
nucleR Resource Report Resource Website 10+ mentions |
nucleR (RRID:SCR_010895) | nucleR | software resource | A R/Bioconductor package for a flexible and fast recognition of nucleosome positioning from next generation sequencing and tiling arrays experiments. The software is integrated with standard high-throughput genomics R packages and allows for in situ visualization as well as to export results to common genome browser formats. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Barcelona; Barcelona; Spain |
PMID:21653521 | OMICS_00511, biotools:nucler | https://bio.tools/nucler | SCR_010895 | 2026-02-14 02:02:06 | 27 | |||||||
|
Genovar Resource Report Resource Website 1+ mentions |
Genovar (RRID:SCR_010930) | Genovar | software resource | A Detection and Visualization software tool for Genomic Variants. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Korea National Institute of Health |
Free, Public | OMICS_00724, biottools:genovar | https://bio.tools/genovar | SCR_010930 | 2026-02-14 02:02:07 | 1 | |||||||
|
ArrayAnalysis.org Resource Report Resource Website 50+ mentions |
ArrayAnalysis.org (RRID:SCR_010932) | ArrayAnalysis.org | data analysis service, analysis service resource, production service resource, service resource, software resource | Tools for microarray quality control and pre-processing. | r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:23620278 | Acknowledgement requested | OMICS_00742, biotools:arrayanalysis.org | https://bio.tools/arrayanalysis.org | SCR_010932 | ArrayAnalysis | 2026-02-14 02:02:08 | 72 | |||||
|
MAnorm Resource Report Resource Website 100+ mentions |
MAnorm (RRID:SCR_010869) | MAnorm | software resource | A robust software package for quantitative comparison of ChIP-Seq data sets. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Dana-Farber Cancer Institute |
PMID:22424423 | OMICS_00467, biotools:manorm | https://bio.tools/manorm | SCR_010869 | Manorm - a robust model for quantitative comparison of ChIP-Seq data sets | 2026-02-14 02:01:51 | 111 | ||||||
|
MeRIP-PF Resource Report Resource Website 1+ mentions |
MeRIP-PF (RRID:SCR_010904) | MeRIP-PF | software resource | A high-efficiency and easy-to-use analysis pipeline for MeRIP-Seq peak-finding at high resolution, which compares distributions of reads between immunoprecipitation sample and control sample. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
biotools:merip-pf, OMICS_00571 | https://bio.tools/merip-pf | SCR_010904 | MeRIP-Seq Peak-Finding Program | 2026-02-14 02:02:07 | 3 | |||||||
|
BatMeth Resource Report Resource Website 1+ mentions |
BatMeth (RRID:SCR_010906) | BatMeth | software resource | Improved mapper for bisulfite sequencing reads on DNA methylation. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Google Code |
biotools:batmeth, OMICS_00574 | https://bio.tools/batmeth | SCR_010906 | 2026-02-14 02:02:06 | 1 | ||||||||
|
QUMA Resource Report Resource Website 100+ mentions |
QUMA (RRID:SCR_010907) | QUMA | software resource | You can easily align, visualize and quantify bisulfite sequence data for CpG methylation analysis. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_00588, biotools:quma | https://bio.tools/quma | SCR_010907 | QUantification tool for Methylation Analysis | 2026-02-14 02:02:06 | 364 | |||||||
|
PeakRanger Resource Report Resource Website 10+ mentions |
PeakRanger (RRID:SCR_010863) | PeakRanger | software resource | Software for a multi-purpose ChIP Seq peak caller. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21554709 | OMICS_00451, biotools:peakranger | https://bio.tools/peakranger | SCR_010863 | 2026-02-14 02:02:06 | 21 | |||||||
|
SEAL Resource Report Resource Website 100+ mentions |
SEAL (RRID:SCR_010914) | SEAL | software resource | A suite of distributed software applications for aligning short DNA reads, and manipulating and analyzing short read alignments. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21697132 | biotools:seal, OMICS_00682 | https://bio.tools/seal | SCR_010914 | 2026-02-14 02:01:51 | 121 | |||||||
|
DIME Resource Report Resource Website 10+ mentions |
DIME (RRID:SCR_010874) | DIME | software resource | R-package for identifying differential ChIP-seq based on an ensemble of mixture models. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
biotools:DIME, OMICS_00473 | https://bio.tools/DIME | SCR_010874 | 2026-02-14 02:02:05 | 29 | ||||||||
|
BWA Resource Report Resource Website 1000+ mentions |
BWA (RRID:SCR_010910) | BWA | sequence analysis software, data processing software, alignment software, data analysis software, software application, software resource, image analysis software | Software for aligning sequencing reads against large reference genome. Consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. First for sequence reads up to 100bp, and other two for longer sequences ranged from 70bp to 1Mbp. | sequence, alignment, reference, genome, human, short, long, read, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: shovill is related to: Proovread is related to: BWA-MEM2 has parent organization: SourceForge is required by: RelocaTE |
PMID:19451168 PMID:20080505 DOI:10.1093/bioinformatics/btp324 |
Free, Available for download, Freely available | SCR_015853, biotools:bwa-sw, OMICS_00654 | https://sourceforge.net/projects/bio-bwa/files/ https://bio.tools/bwa-sw https://sources.debian.org/src/bwa/ |
SCR_010910 | Burrows-Wheeler Aligner (BWA), Burrows-Wheeler Aligner | 2026-02-14 02:01:51 | 2291 | |||||
|
CloudBurst Resource Report Resource Website |
CloudBurst (RRID:SCR_010911) | CloudBurst | software resource | A new parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:19357099 | Free | OMICS_00657, biotools:cloudburst | https://bio.tools/cloudburst | SCR_010911 | 2026-02-14 02:02:06 | 0 | ||||||
|
Integrative Genomics Viewer Resource Report Resource Website 500+ mentions |
Integrative Genomics Viewer (RRID:SCR_011793) | IGV | software resource | A high-performance visualization tool for interactive exploration of large, integrated genomic datasets. | genomic datasets exploration, |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Broad Institute |
DOI:10.1038/nbt.1754 | OMICS_00917, biotools:igv | https://bio.tools/igv https://sources.debian.org/src/igv/ |
SCR_011793 | 2026-02-14 02:02:14 | 809 | |||||||
|
NCBI Genome Workbench Resource Report Resource Website 10+ mentions |
NCBI Genome Workbench (RRID:SCR_011794) | Genome Workbench | software resource | An integrated application for viewing and analyzing sequence data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: NCBI |
OMICS_00920, biotools:ncbi_genome_workbench | https://bio.tools/ncbi_genome_workbench | SCR_011794 | 2026-02-14 02:02:27 | 11 | ||||||||
|
ngs.plot Resource Report Resource Website 10+ mentions |
ngs.plot (RRID:SCR_011795) | ngs.plot | software resource | A software program that allows you to easily visualize your next-generation sequencing (NGS) samples at functional genomic regions. | bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
GNU General Public License, v3 | BioTools:ngs.plot, OMICS_00922, biotools:ngs.plot | https://bio.tools/ngs.plot https://bio.tools/ngs.plot https://bio.tools/ngs.plot |
SCR_011795 | ngsplot, ngsplot - Quick mining and visualization of next-generation sequencing data by integrating genomic databases | 2026-02-14 02:02:05 | 42 | ||||||
|
MizBee Resource Report Resource Website 1+ mentions |
MizBee (RRID:SCR_011804) | MizBee | software resource | A multiscale synteny browser for exploring conservation relationships in comparative genomics data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Utah; Utah; USA |
OMICS_00943, biotools:mizbee | https://bio.tools/mizbee | SCR_011804 | MizBee - A Multiscale Synteny Browser | 2026-02-14 02:02:05 | 2 | |||||||
|
CANGS Resource Report Resource Website 1+ mentions |
CANGS (RRID:SCR_011837) | CANGS | data analysis software, software resource, data processing software, software application | A user-friendly utility for processing and analyzing 454 GS-FLX data in biodiversity studies. | windows, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
PMID:20180949 | biotools:cangs, OMICS_01084 | https://bio.tools/cangs | SCR_011837 | 2026-02-14 02:02:05 | 1 |
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