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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
CGHseg Resource Report Resource Website 1+ mentions |
CGHseg (RRID:SCR_010922) | CGHseg | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. Software R package dedicated to the analysis of CGH profiles using segmentation models. | is listed by: OMICtools | PMID:21209153 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00712 | SCR_010922 | 2026-02-14 02:01:51 | 1 | ||||||||
|
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 | ||||||
|
BASE Resource Report Resource Website 500+ mentions |
BASE (RRID:SCR_010937) | BASE | software resource | A comprehensive management application for information, data, and analysis of microarray experiments, available as free open source software. |
is listed by: OMICtools is listed by: SoftCite has parent organization: Lund University; Lund; Sweden |
PMID:19822003 | GNU General Public License, v3 | OMICS_00749 | SCR_010937 | BASE - BioArray Software Environment, BioArray Software Environment | 2026-02-14 02:02:07 | 506 | |||||||
|
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 | ||||||
|
mCarts Resource Report Resource Website 1+ mentions |
mCarts (RRID:SCR_010902) | mCarts | software resource | A hidden Markov model (HMM)-based software to predict clusters RNA motif sites. |
is listed by: OMICtools has parent organization: Columbia University; New York; USA |
PMID:23685613 | Apache License | OMICS_00567 | SCR_010902 | 2026-02-14 02:02:06 | 4 | ||||||||
|
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 | |||||||
|
B-SOLANA Resource Report Resource Website |
B-SOLANA (RRID:SCR_010905) | B-SOLANA | software resource | An approach for the analysis of two-base encoding bisulfite sequencing data. |
is listed by: OMICtools has parent organization: Google Code |
OMICS_00573 | SCR_010905 | 2026-02-14 02:01:51 | 0 | ||||||||||
|
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 | |||||||
|
NEXT-peak Resource Report Resource Website 1+ mentions |
NEXT-peak (RRID:SCR_010862) | NEXT-peak | software resource | A software program to call peaks from ChIP-seq data for transcription factor binding sites. |
is listed by: OMICtools has parent organization: Old Dominion University; Virginia; USA |
PMID:23706083 | OMICS_00450 | SCR_010862 | 2026-02-14 02:02:05 | 1 | |||||||||
|
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 | |||||||
|
RRBSMAP Resource Report Resource Website 1+ mentions |
RRBSMAP (RRID:SCR_010864) | RRBSMAP | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18,2023. A specifically designed version of BSMAP for reduced representation bisulfite sequencing (RRBS). |
is listed by: OMICtools has parent organization: Google Code |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00589 | SCR_010864 | 2026-02-14 02:02:06 | 5 | |||||||||
|
SIPeS Resource Report Resource Website 1+ mentions |
SIPeS (RRID:SCR_010865) | SIPeS | software resource | An algorithm that allows researchers to identify transcript factor binding sites from paired-end sequencing reads. SIPeS uses a dynamic baseline directly through the piling up of fragments to effectively find peaks, overcoming the disadvantage of estimating the average length of DNA fragments from singled-end sequencing achieving more powerful prediction binding sites with high sensitivity and specificity. | is listed by: OMICtools | PMID:20144209 | Free to academic users, Non-commercial, Commercial requires permission | OMICS_00462 | SCR_010865 | SIPeS - Site Identification from Paired-end Sequencing, Site Identification from Paired-end Sequencing | 2026-02-14 02:01:50 | 5 | |||||||
|
T-PIC Resource Report Resource Website 1+ mentions |
T-PIC (RRID:SCR_010867) | T-PIC | software resource | A software for determining DNA/protein binding sites from a ChIP-Seq experiment. |
is listed by: OMICtools has parent organization: University of Miami; Florida; USA |
OMICS_00464 | SCR_010867 | 2026-02-14 02:02:06 | 7 | ||||||||||
|
ChIPDiff Library Comparison Resource Report Resource Website |
ChIPDiff Library Comparison (RRID:SCR_010871) | ChIPDiff Library Comparison | software resource | Provides a solution for the identification of Differential Histone Modification Sites (DHMSs) by comparing two ChIP-seq libraries (L1 and L2). | is listed by: OMICtools | OMICS_00469 | SCR_010871 | 2026-02-14 02:02:06 | 0 | ||||||||||
|
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 |
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