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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
TEMP Resource Report Resource Website 100+ mentions |
TEMP (RRID:SCR_001788) | software resource | Software package for detecting transposable elements (TEs) insertions and excisions from pooled high-throughput sequencing data. | standalone software, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Massachusetts Medical School; Massachusetts; USA |
PMID:24753423 | Free, Available for download, Freely available | OMICS_03821, biotools:temp | https://bio.tools/temp | SCR_001788 | 2026-02-14 02:00:11 | 211 | |||||||
|
AffyPipe Resource Report Resource Website 1+ mentions |
AffyPipe (RRID:SCR_002032) | software resource | An open-source software pipeline for Affymetrix Axiom genotyping workflow. | affymetrix, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
Italian Ministry of Education University and Research 505/Ric; project GenHome ; European Union FP7 project Gene2Farm 289592 |
PMID:25028724 | Free, Available for download, Freely available | biotools:affypipe, OMICS_05203 | https://bio.tools/affypipe | SCR_002032 | AffyPipe: an open-source pipeline for Affymetrix Axiom genotyping workflow | 2026-02-14 02:00:17 | 5 | |||||
|
CanSNPer Resource Report Resource Website 10+ mentions |
CanSNPer (RRID:SCR_001980) | software resource | Software that is a hierarchical genotype classifier of clonal pathogens. | python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24574113 | Free, Available for download, Freely available | biotools:cansnper, OMICS_03706 | https://bio.tools/cansnper | SCR_001980 | 2026-02-14 02:00:16 | 18 | |||||||
|
Ray Resource Report Resource Website 1+ mentions |
Ray (RRID:SCR_001916) | Ray | software resource | Software that assembles reads obtained with new sequencing technologies (Illumina, 454, SOLiD) using MPI 2.2. | mpi, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:20958248 DOI:10.1089/cmb.2009.0238 |
Free, Available for download, Freely available | OMICS_00027, biotools:ray | https://bio.tools/ray https://sources.debian.org/src/ray/ |
SCR_001916 | Ray - a de novo assembler using MPI 2.2, Ray - Parallel genome assemblies for parallel DNA sequencing | 2026-02-14 02:00:11 | 1 | |||||
|
GEMINI Resource Report Resource Website 500+ mentions |
GEMINI (RRID:SCR_014819) | software resource | Framework for exploring genetic variation in the context of the genome annotations available for the human genome. Users can load a VCF file into a database and each variant is automatically annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks, OMIM, dbSNP, KEGG, and HPRD. | framework, genetic variation, annotation, human, genome, vcf, database, , bio.tools, FASEB list |
uses: KEGG uses: ENCODE uses: OMIM uses: dbSNP uses: HPRD - Human Protein Reference Database is listed by: Debian is listed by: bio.tools has parent organization: University of Utah; Utah; USA |
DOI:10.1371/journal.pcbi.1003153 | Freely available | biotools:gemini | https://github.com/arq5x/gemini https://bio.tools/gemini |
SCR_014819 | GEnome MINIng (GEMINI), GEMINI - a flexible framework for exploring genome variation, Genome Mining, GEnome MINIng | 2026-02-14 02:03:02 | 515 | ||||||
|
Laniakea Resource Report Resource Website 1+ mentions |
Laniakea (RRID:SCR_018146) | software resource | Software tool for automatic deployment of virtual Galaxy environments for life science. Can be deployed over common cloud architectures supported both by public and private e-infrastructures. User interacts with Laniakea based service through simple front end that allows general setup of Galaxy instance, then Laniakea takes care of automatic deployment of virtual hardware and software components. User gains access with full administrative privileges to private, production grade, fully customized, Galaxy virtual instance, and to underlying virtual machine. | Automatic deployment, virtual Galaxy, life science environment, virtual machine, cloud architecture, Elixir Italy, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: ELIXIR Tools and Data Services Registry |
Restricted | biotools:Laniakea | https://bio.tools/Laniakea | SCR_018146 | Galaxy cloud on demand workflow workbench | 2026-02-14 02:03:34 | 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 | 2026-02-14 02:02:23 | 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 | 2026-02-14 02:02:16 | 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 | 2026-02-14 02:02:18 | 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 | 2026-02-14 02:02:44 | 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 | 2026-02-14 02:02:24 | 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 | 2026-02-14 02:02:48 | 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 | 2026-02-14 02:02:24 | 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 | 2026-02-14 02:02:25 | 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 | 2026-02-14 02:02:45 | 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 | 2026-02-14 02:02:46 | 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 | 2026-02-14 02:02:27 | 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 | 2026-02-14 02:02:27 | 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 | 2026-02-14 02:02:47 | 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 | 2026-02-14 02:02:28 | 0 |
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