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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
MToolBox Resource Report Resource Website 50+ mentions |
MToolBox (RRID:SCR_012112) | software resource | Software for a highly automated bioinformatics pipeline to reconstruct and analyze human mitochondrial DNA from high throughput sequencing data. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25028726 | GNU General Public License | OMICS_05466, biotools:mtoolbox | https://bio.tools/mtoolbox | SCR_012112 | 2026-08-01 12:04:33 | 56 | |||||||
|
Allim Resource Report Resource Website 1+ mentions |
Allim (RRID:SCR_012114) | software resource | A user-friendly software tool to estimate allele-specific gene expression. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:23615333 | biotools:allim, OMICS_05504 | https://bio.tools/allim | SCR_012114 | 2026-08-01 12:04:33 | 2 | ||||||||
|
NAIL Resource Report Resource Website 1+ mentions |
NAIL (RRID:SCR_012134) | software resource | A set of software tools to simplify the range of computational activities involved in regulatory network inference. It is technology-independent and includes an interface layer to allow easy integration of components into other applications. It is implemented in MATLAB and is available for all researchers to use. | standalone software, mac os x, unix/linux, windows, matlab, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:25246431 | Apache License | OMICS_05868, biotools:nail | https://bio.tools/nail | SCR_012134 | Network Analysis and Inference Library | 2026-08-01 12:04:35 | 8 | ||||||
|
LocalAli Resource Report Resource Website 1+ mentions |
LocalAli (RRID:SCR_012147) | software resource | A fast and scalable local network alignment software tool for the identification of functionally conserved modules in multiple networks. LocalAli outperforms all existing algorithms in terms of coverage, consistency and scalability, meanwhile retains a high precision in the identification of functionally coherent subnetworks. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:25282642 | GNU General Public License | biotools:localali, OMICS_06337 | https://bio.tools/localali | SCR_012147 | 2026-08-01 12:04:36 | 1 | |||||||
|
Isaac Resource Report Resource Website 50+ mentions |
Isaac (RRID:SCR_012772) | Isaac | software resource | Whole genome secondary analysis on Illumina sequencing platforms. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
biotools:isaac, OMICS_00289 | https://bio.tools/isaac | SCR_012772 | 2026-08-01 12:04:40 | 66 | ||||||||
|
lumi Resource Report Resource Website 100+ mentions |
lumi (RRID:SCR_012781) | lumi | software resource | Software that provides an integrated solution for the Illumina microarray data analysis. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is listed by: SoftCite has parent organization: Bioconductor |
biotools:lumi, OMICS_00770 | https://bio.tools/lumi | SCR_012781 | 2026-08-01 12:04:51 | 318 | ||||||||
|
Ngs backbone Resource Report Resource Website 1+ mentions |
Ngs backbone (RRID:SCR_012907) | Ngs_backbone | software resource | A bioinformatic application created to work on sequence analysis by using NGS (Next Generation Sequencing) and sanger sequences. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
biotools:ngs_backbone, OMICS_01132 | https://bio.tools/ngs_backbone | SCR_012907 | 2026-08-01 12:04:41 | 1 | ||||||||
|
rqubic Resource Report Resource Website |
rqubic (RRID:SCR_012869) | rqubic | software resource | This software package implements the QUBIC algorithm for the qualitative biclustering with gene expression data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:19509312 | Free | biotools:rqubic, OMICS_01799 | https://bio.tools/rqubic | SCR_012869 | rqubic - Qualitative biclustering algorithm for expression data analysis in R | 2026-08-01 12:04:52 | 0 | |||||
|
DiffBind Resource Report Resource Website 1000+ mentions |
DiffBind (RRID:SCR_012918) | DiffBind | software resource | Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
biotools:diffbind, OMICS_00471 | https://bio.tools/diffbind | SCR_012918 | Differential Binding Analysis of ChIP-Seq peak data | 2026-08-01 12:04:53 | 1254 | |||||||
|
eisa Resource Report Resource Website 1+ mentions |
eisa (RRID:SCR_012883) | eisa | software resource | A biclustering method; it finds correlated blocks (transcription modules) in gene expression (or other tabular) data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free | OMICS_01801, biotools:eisa | https://bio.tools/eisa | SCR_012883 | eisa - Expression data analysis via the Iterative Signature Algorithm | 2026-08-01 12:04:52 | 2 | ||||||
|
Trowel Resource Report Resource Website 1+ mentions |
Trowel (RRID:SCR_012890) | Trowel | software resource | An error correction module for Illumina sequencing reads, which is based on the k-mer spectrum approach. | c++, illumina, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
Apache License | OMICS_01111, biotools:trowel | https://bio.tools/trowel/ | SCR_012890 | Trowel - Error Correction Module for Illumina Sequencing Reads, Trowel - Sequencing Error Corrector | 2026-08-01 12:04:42 | 5 | ||||||
|
CSAR Resource Report Resource Website 10+ mentions |
CSAR (RRID:SCR_012930) | CSAR | software resource | Statistical tools for the analysis of ChIP-seq data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:21554688 | Free | OMICS_00435, biotools:csar | https://bio.tools/csar | SCR_012930 | 2026-08-01 12:04:53 | 49 | ||||||
|
SeqPrep Resource Report Resource Website 500+ mentions |
SeqPrep (RRID:SCR_013004) | SeqPrep | software resource | A program to merge paired end Illumina reads that are overlapping into a single longer read. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
biotools:seqprep, OMICS_01092 | https://bio.tools/seqprep, https://sources.debian.org/src/seqprep/ | SCR_013004 | SeqPrep - Tool for stripping adaptors and/or merging paired reads with overlap into single reads | 2026-08-01 12:04:43 | 977 | |||||||
|
phyloseq Resource Report Resource Website 1000+ mentions |
phyloseq (RRID:SCR_013080) | phyloseq | software resource | Software for handling and analysis of high-throughput microbiome census data. | bio.tools |
is used by: microViz is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
DOI:10.1371/journal.pone.0061217 | OMICS_01520, biotools:phyloseq | https://bio.tools/phyloseq, https://sources.debian.org/src/r-bioc-phyloseq/ | SCR_013080 | 2026-08-01 12:04:45 | 2774 | |||||||
|
AMOS Resource Report Resource Website 1000+ mentions |
AMOS (RRID:SCR_013067) | AMOS | software resource | A collection of tools and class interfaces for the assembly of DNA reads. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
DOI:10.1093/bib/bbr074 | OMICS_00008, biotools:amos | https://bio.tools/amos, https://sources.debian.org/src/ampliconnoise/ | SCR_013067 | 2026-08-01 12:04:55 | 4769 | |||||||
|
Reptile Resource Report Resource Website 10+ mentions |
Reptile (RRID:SCR_013075) | Reptile | software resource | A software developed in C++ for correcting sequencing errors in short reads from next-gen sequencing platforms. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:20834037 | biotools:reptile, OMICS_01109 | https://bio.tools/reptile | SCR_013075 | 2026-08-01 12:04:55 | 30 | |||||||
|
ChimeraSlayer Resource Report Resource Website 100+ mentions |
ChimeraSlayer (RRID:SCR_013283) | ChimeraSlayer | software resource | A chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp). | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
OMICS_01113, biotools:chimeraslayer | https://bio.tools/chimeraslayer | SCR_013283 | 2026-08-01 12:04:46 | 319 | ||||||||
|
Telescoper Resource Report Resource Website |
Telescoper (RRID:SCR_013206) | Telescoper | software resource | An algorithm that iteratively extends long paths through a series of read-overlap graphs and evaluates them based on a statistical framework. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:22962446 | biotools:telescoper, OMICS_00036 | https://bio.tools/telescoper | SCR_013206 | Telescoper - De novo assembly algorithm | 2026-08-01 12:04:45 | 0 | ||||||
|
IsoLasso Resource Report Resource Website 1+ mentions |
IsoLasso (RRID:SCR_013176) | IsoLasso | software resource | An algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
OMICS_01320, biotools:isolasso | https://bio.tools/isolasso | SCR_013176 | 2026-08-01 12:04:46 | 3 | ||||||||
|
HeurAA Resource Report Resource Website |
HeurAA (RRID:SCR_013212) | HeurAA | software resource | Software for accurate and fast detection of genetic variations with a novel heuristic amplicon aligner program for next generation sequencing. | unix/linux, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23349847 | OMICS_00097, biotools:heuraa | https://bio.tools/heuraa | SCR_013212 | heurAA - NGS multiplexed amplicon aligner | 2026-08-01 12:04:56 | 0 |
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