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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
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 | 2026-07-25 12:07:08 | 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 | 2026-07-25 12:07:06 | 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 | 2026-07-25 12:07:08 | 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 | 2026-07-25 12:07:04 | 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 | 2026-07-25 12:07:06 | 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 | 2026-07-25 12:07:04 | 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 | 2026-07-25 12:07:06 | 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 | 2026-07-25 12:07:08 | 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 | 2026-07-25 12:07:04 | 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 | 2026-07-25 12:07:08 | 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 | 2026-07-25 12:07:04 | 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 | 2026-07-25 12:07:07 | 121 | |||||||
|
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 | 2026-07-25 12:07:09 | 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 | 2026-07-25 12:07:09 | 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 | 2026-07-25 12:07:06 | 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 | 2026-07-25 12:07:04 | 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 | 2026-07-25 12:07:04 | 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 | 2026-07-25 12:07:06 | 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 | 2026-07-25 12:07:09 | 46 | ||||||||||
|
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 | 2026-07-25 12:07:08 | 83 |
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