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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | 2026-02-07 02:08:06 | 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 | 2026-02-07 02:08:03 | 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 | 2026-02-07 02:08:06 | 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 | 2026-02-07 02:07:54 | 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 | 2026-02-07 02:07:55 | 119 | |||||||
|
aCGHtool Resource Report Resource Website 1+ mentions |
aCGHtool (RRID:SCR_010915) | aCGHtool | software resource | A software tool for the normalization, visualization, breakpoint detection, and comparative analysis of array-CGH data which allows the accurate and sensitive detection of CNAs. | is listed by: OMICtools | OMICS_00699 | SCR_010915 | 2026-02-07 02:08:04 | 1 | ||||||||||
|
Agilent Genomic Workbench Resource Report Resource Website 100+ mentions |
Agilent Genomic Workbench (RRID:SCR_010918) | Agilent Genomic Workbench | software resource | A comprehensive design and analysis tool for setting up and interpreting your microarray experiments. | is listed by: OMICtools | OMICS_00702 | SCR_010918 | 2026-02-07 02:08:07 | 248 | ||||||||||
|
DBChIP Resource Report Resource Website 1+ mentions |
DBChIP (RRID:SCR_010872) | DBChIP | software resource | Detects differential binding of transcription factors with ChIP-seq. | is listed by: OMICtools | OMICS_00470 | SCR_010872 | 2026-02-07 02:08:03 | 5 | ||||||||||
|
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 | 2026-02-07 02:07:54 | 29 | ||||||||
|
ChIPModule Resource Report Resource Website 1+ mentions |
ChIPModule (RRID:SCR_010877) | ChIPModule | software resource | A software tool for systematic discovery of transcription factors and their cofactors from ChIP-seq data. | is listed by: OMICtools | OMICS_00477 | SCR_010877 | ChIPModule: Systematic discovery of transcription factors and their cofactors from ChIP-seq data | 2026-02-07 02:07:54 | 1 | |||||||||
|
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 | 2026-02-07 02:08:04 | 0 | ||||||
|
ERNE Resource Report Resource Website 10+ mentions |
ERNE (RRID:SCR_010912) | ERNE | software resource | A short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00662 | SCR_010912 | 2026-02-07 02:07:55 | 43 | ||||||||||
|
F-Seq Resource Report Resource Website 50+ mentions |
F-Seq (RRID:SCR_010880) | F-Seq | software resource | A software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites whose output can be displayed directly in the UCSC Genome Browser. |
is listed by: OMICtools has parent organization: University of North Carolina at Chapel Hill; North Carolina; USA |
OMICS_00482 | SCR_010880 | 2026-02-07 02:08:06 | 83 | ||||||||||
|
ABySS-Explorer Resource Report Resource Website 1+ mentions |
ABySS-Explorer (RRID:SCR_010980) | ABySS-Explorer | software resource | An interactive Java application that employs a novel graph-based representation to display a sequence assembly and associated meta data. | is listed by: OMICtools | OMICS_00873 | SCR_010980 | 2026-02-07 02:07:57 | 3 | ||||||||||
|
DNPTrapper Resource Report Resource Website |
DNPTrapper (RRID:SCR_010981) | DNPTrapper | software resource | An assembly editing and visualization tool specifically designed for manual analysis and finishing of repeated regions. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:16549006 | OMICS_00881 | SCR_010981 | 2026-02-07 02:08:08 | 0 | ||||||||
|
Hawkeye Resource Report Resource Website 1+ mentions |
Hawkeye (RRID:SCR_010982) | Hawkeye | software resource | A visual analytics tool for genome assembly analysis and validation, designed to aid in identifying and correcting assembly errors. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00884 | SCR_010982 | 2026-02-07 02:08:05 | 9 | ||||||||||
|
MetExtract Resource Report Resource Website 10+ mentions |
MetExtract (RRID:SCR_012048) | software resource | A software tool for scientists working with stable isotopic labelling and high resolution liquid chromatography mass spectrometry. | c++ |
is listed by: OMICtools has parent organization: Google Code |
PMID:22238263 | MIT License | OMICS_02639 | SCR_012048 | 2026-02-07 02:08:21 | 13 | ||||||||
|
MZmine Resource Report Resource Website 500+ mentions |
MZmine (RRID:SCR_012040) | software resource | Software for mass-spectrometry data processing, with the main focus on LC-MS data. | standalone software |
is listed by: OMICtools has parent organization: SourceForge |
PMID:20650010 | Open unspecified license | OMICS_02385 | SCR_012040 | 2026-02-07 02:08:29 | 788 | ||||||||
|
Gene ARMADA Resource Report Resource Website |
Gene ARMADA (RRID:SCR_012006) | Gene ARMADA | software resource | Software for the analysis of microarray data with a MATLAB implemented platform with a GUI that integrates all steps of microarray data analysis including automated data import, noise correction, filtering, normalization, statistical testing, clustering, classification and annotation. | javascript |
is listed by: OMICtools has parent organization: Google Code |
PMID:19860866 | New BSD License, Acknowledgement requested | OMICS_01821 | SCR_012006 | Gene Automated Robust MicroArray Data Analysis, Gene ARMADA: robust automated pipelines for the analysis of microarray data, Gene ARMADA (Automated Robust MicroArray Data Analysis), Gene ARMADA: MATLAB software for the analysis of microarray data | 2026-02-07 02:08:20 | 0 | ||||||
|
International Society for Computational Biology Resource Report Resource Website 10+ mentions |
International Society for Computational Biology (RRID:SCR_012009) | ISCB | nonprofit organization | Community building portal that serves over 3,000 members from more than 70 countries by addressing scientific policies, providing access to high quality publications, organizing meetings, and serving as a portal to information about training, education, employment, etc. | is listed by: OMICtools | OMICS_01827, Wikidata: Q4288281, grid.420343.2, ISNI: 0000 0000 8673 7548 | https://ror.org/01jv71z12 | SCR_012009 | International Society for Computational Biology | 2026-02-07 02:08:28 | 37 |
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