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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ICPL ESIQuant Resource Report Resource Website |
ICPL ESIQuant (RRID:SCR_012047) | software resource | A proteomics software tool for quantitatively analyzing large mass spectrometric datasets acquired from ICPL based proteomics experiments. | standalone software, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:23454610 | biotools:icpl_esiquant, OMICS_02490 | https://bio.tools/icpl_esiquant | SCR_012047 | 2026-08-01 12:04:29 | 0 | ||||||||
|
easyRNASeq Resource Report Resource Website 10+ mentions |
easyRNASeq (RRID:SCR_012020) | easyRNASeq | software resource | Software that calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as ''RPKM'' or by the ''DESeq'' or ''edgeR'' package. | rna-seq, gene expression, genetics, preprocessing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor has parent organization: European Molecular Biology Laboratory |
PMID:22847932 | Artistic License, v2 | OMICS_01938, biotools:easyrnaseq | https://bio.tools/easyrnaseq | SCR_012020 | easyRNASeq - Count summarization and normalization for RNA-Seq data | 2026-08-01 12:04:28 | 29 | |||||
|
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 | |||||||
|
MS-GF+ Resource Report Resource Website 100+ mentions |
MS-GF+ (RRID:SCR_015646) | software resource | Software that performs peptide identification by scoring MS/MS spectra against peptides derived from a protein sequence database. | protein idenitification, peptide sequence, ms, ms spectrum, proteomic, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools has parent organization: Pacific Northwest National Laboratory |
NCRR RR018522; NCRR 1-P41-RR024851; NIAID ; W.R. Wiley Environmental Molecular Science Laboratory |
PMID:25358478 | Free, Available for download, Acknowledgment requested | biotools:ms-gf | https://github.com/sangtaekim/msgfplus, https://bio.tools/ms-gf | SCR_015646 | MSGF+, MSGFPlus | 2026-08-01 12:05:26 | 155 | |||||
|
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 |
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