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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Bowtie 2 Resource Report Resource Website 1000+ mentions |
Bowtie 2 (RRID:SCR_016368) | sequence analysis software, software resource, image analysis software, alignment software, data analysis software, data processing software, software application | Ultrafast and memory efficient tool for aligning sequencing reads to long reference sequences. Supports gapped, local, and paired end alignment modes. More suited to finding longer, gapped alignments in comparison with original Bowtie method. | sequence, analysis, long, reference, sequence, read, alignment, gap, local, pair, end, rna, rnaseq, bio.tools |
is used by: HLA-HD is listed by: Debian is listed by: bio.tools is listed by: SoftCite is related to: Bowtie |
NHGRI R01 HG006102; NIGMS R01 GM083873 |
PMID:22388286 | Free, Available for download, Freely available | biotools:bowtie2 | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml, https://github.com/BenLangmead/bowtie2, https://bio.tools/bowtie2 | SCR_016368 | , bowtie 2, bowtie2 v 2.2.3 | 2026-08-06 09:28:25 | 1745 | |||||
|
Off-Spotter Resource Report Resource Website 10+ mentions |
Off-Spotter (RRID:SCR_015739) | web application, algorithm resource, software resource | Web application that identifies genomic instances for a given combination of gRNA(s), PAM, number of mismatches, and seed. This tool is limited to a single 1,000 nucleotides sequence or fewer than twenty CR-separated 20-mers. | CRISPR, Cas, sgrna, prokaryotic immune system, genetic engineering, bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: Thomas Jefferson University; Pennsylvania; USA |
William M. Keck Foundation | PMID:25630343 | Freely available, Free, Available for download, Tutorial available | biotools:off-spotter | https://bio.tools/off-spotter | SCR_015739 | Off-Spotter: tool for CRISPR/Cas design, Off-spotter sgRNA algorithm | 2026-08-06 09:28:41 | 43 | |||||
|
GEN3VA Resource Report Resource Website 1+ mentions |
GEN3VA (RRID:SCR_015682) | data analysis software, software application, software resource, data processing software | Software tool for aggregation and analysis of gene expression signatures from related studies.Used to aggregate and analyze gene expression signatures extracted from GEO by crowd using GEO2Enrichr. Used to view aggregated report that provides global, interactive views, including enrichment analyses, for collections of signatures from multiple studies sharing biological theme. | GEO2Enrichr, gene expression signatures, enrichment analyses, multiple studies, biological theme, bio.tools |
is listed by: bio.tools is listed by: Debian works with: Gene Expression Omnibus (GEO) |
NHLBI U54 HL127624; NCI U54 CA189201; NIGMS R01 GM098316 |
PMID:27846806 | Free, Freely available | biotools:gen3va | https://github.com/MaayanLab/gen3va, https://bio.tools/gen3va | SCR_015682 | GENE Expression and Enrichment Vector Analyzer | 2026-08-06 09:28:42 | 5 | |||||
|
BCBtoolkit Resource Report Resource Website 50+ mentions |
BCBtoolkit (RRID:SCR_015519) | software resource, data analysis software, software toolkit, data processing software, software application | Software toolkit that provides several multi-modal tools to assess brain disconnections and remote effects of lesions. All modules are designed to process brain lesion data with a normalization algorithm, a module to estimate the probability and the severity of white matter disconnections, and a tool to build a map of the disconnected areas. | brain lesion, brain disconnection, white matter, bio.tools |
is listed by: bio.tools is listed by: Debian is related to: NIH Human Connectome Project |
Open source, Free, Available for download, Available on Mac OS, Available on Linux | biotools:bcbtoolkit | https://bio.tools/bcbtoolkit | SCR_015519 | BCBtoolkit 4.0 | 2026-08-06 09:28:39 | 58 | |||||||
|
Atac Resource Report Resource Website 1000+ mentions |
Atac (RRID:SCR_015980) | sequence analysis software, software resource, image analysis software, alignment software, data analysis software, data processing software, software application | Alignment analysis software tool for comparative mapping between two genome assemblies or between two different genomes. It can cache intermediate results to speed a comparisons of multiple sequences. | software, tool, DNA, sequence, analysis, aligning, genome, compare, mapping, assembly, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1093/bioinformatics/btr285 | Free, Freely available, Available for download | OMICS_29044, biotools:atac | https://bio.tools/atac, https://sources.debian.org/src/atac/ | SCR_015980 | 2026-08-06 09:28:46 | 1748 | |||||||
|
Bamtools Resource Report Resource Website 100+ mentions |
Bamtools (RRID:SCR_015987) | software resource, data analysis software, data management software, software toolkit, data processing software, software application | Software that provides both a C++ API and a command-line toolkit for reading, writing, and manipulating genome sequence alignment files in the BAM and SAM formats. It is used for research analysis and management of data produced by sequencing technologies. | c++, api, sam, bam genome, sequence, alignment, data, analysis, management, command, manipulation, binary, map, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01 HG004719; NHGRI RC2 HG005552 |
PMID:21493652 DOI:10.1093/bioinformatics/btr174 |
biotools:bamtools, OMICS_11315 | https://bio.tools/bamtools, https://sources.debian.org/src/bamtools/ | SCR_015987 | API:Application Programming Interface, BAM:Binary Alignment Map, SAM:Sequence Alignment Map | 2026-08-06 09:28:46 | 324 | ||||||
|
scater Resource Report Resource Website 100+ mentions |
scater (RRID:SCR_015954) | sequence analysis software, software resource, data analysis software, software toolkit, data processing software, data visualization software, software application | Software toolkit for doing various analyses of single-cell RNA-seq gene expression data, with a focus on quality control. This package facilitates pre-processing, quality control, normalization and visualization of scRNA-seq data. | scRNA-seq, rna, rnaseq, single, cell, analysis, gene, expression, quality, control, preprocessing, normalization, visualization, r, bio.tools |
is listed by: Debian is listed by: bio.tools |
National Health and Medical Research Council of Australia APP1112681; European Molecular Biology Laboratory ; Cancer Research UK A17197; United Kingdom Medical Research Council ; Oxford Single Cell Biology Consortium |
Free, Available for download | biotools:scater | https://bioconductor.org/packages/scater/, https://bio.tools/scater | SCR_015954 | scater (single-cell analysis toolkit for gene expression data in R) | 2026-08-06 09:28:47 | 173 | ||||||
|
ALTER Resource Report Resource Website 100+ mentions |
ALTER (RRID:SCR_015968) | sequence analysis software, software resource, image analysis software, alignment software, data analysis software, data processing software, web application, software application | Web application to perform program-oriented conversion of DNA and protein alignments and transform between multiple sequence alignment formats. ALTER focuses on the specifications of mainstream alignment and analysis programs rather than on the conversion among more or less specific formats. | Alignment conversion, genome, sequence, DNA, protein, format alignment, phylogenetics, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
European Research Council ERC-2007-Stg 203161-PHYGENOM to D.P.; Spanish Ministry of Science and Education BFU2009-08611 to D.P.; Xunta de Galicia PGIDIT07PXIB310202PR to D.P.; INBIOMED initiative ; University of Vigo 09VIB10 to F.F-.R. |
PMID:20439312 DOI:10.1093/nar/gkq321 |
Freely available, Free, Available for download | OMICS_19786, biotools:alter | https://github.com/sing-group/ALTER, https://bio.tools/alter, https://sources.debian.org/src/alter-sequence-alignment/ | SCR_015968 | ALTER: ALignment Transformation EnviRonment, ALignment Transformation EnviRonment | 2026-08-06 09:28:47 | 112 | |||||
|
LoRDEC Resource Report Resource Website 100+ mentions |
LoRDEC (RRID:SCR_015814) | sequence analysis software, software resource, data analysis software, data processing software, software application | Software that performs hybrid error correction for long, PacBio reads. LoRDEC can correct insertions, deletions, and substitutions in PacBio reads. | hybrid error correction, pacbio read, long error correction, real-time sequencing, bio.tools |
is listed by: Debian is listed by: bio.tools |
Academy of Finland 267591; ANR Colib’read ANR-12-BS02-0008 |
PMID:25165095 | Free, Available for download | biotools:lordec | https://bio.tools/lordec | SCR_015814 | 2026-08-06 09:28:44 | 206 | ||||||
|
UALCAN Resource Report Resource Website 1000+ mentions |
UALCAN (RRID:SCR_015827) | sequence analysis software, software resource, data analysis software, data or information resource, data processing software, web application, software application, database | Web application and database for analyzing cancer transcriptome data. It also has applications is facilitating tumor subgroup gene expression and survival analyses. | tumor, gene expression, survival analysis, cancer transcriptome data, sequencing, biomarker, bio.tools, FASEB list |
is listed by: Debian is listed by: bio.tools |
PMID:28732212 | Freely available | biotools:UALCAN | https://bio.tools/UALCAN | SCR_015827 | 2026-08-06 09:28:42 | 2853 | |||||||
|
circlncRNAnet Resource Report Resource Website 10+ mentions |
circlncRNAnet (RRID:SCR_015794) | software resource, data processing resource, data or information resource, web application, database | Web application for mapping functional networks of long or circular forms of non-coding RNAs. It supports the uploading and processing of user-defined NGS-based gene expression matrix data. | mapping, long form, circular form, non-coding rna, rna mapping, regulatory rna, ncRNA, bio.tools, FASEB list |
is listed by: bio.tools is listed by: Debian requires: RStudio |
Freely available, Free, Available for download, Runs on Linux, Demo available, Tutorial available | biotools:circlncrnanet | https://github.com/smw1414/circlncRNAnet, https://bio.tools/circlncrnanet | SCR_015794 | 2026-08-06 09:28:44 | 31 | ||||||||
|
VaDiR Resource Report Resource Website 10+ mentions |
VaDiR (RRID:SCR_015797) | VaDiR | sequence analysis software, software resource, algorithm resource, data analysis software, data processing software, software application | Method for uncovering mutations from RNA sequencing datasets that could be useful in further functional analysis. It also allows orthogonal validation of DNA-based mutation discovery by providing complementary sequence variation analysis from paired RNA/DNA sequencing data sets. | rna-seq, somatic variant calling, ovarian cancer, cancer genomes transcriptome, orthogonal validation, genetic mutation, sequence variation analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
NCI P30 CA168524; Department of Defense Ovarian Cancer Research Program W81XWH-10-1-0386; University of Kansas Endowment Association ; Biostatistics and Informatics Shared Resource (BISR) ; Cancer Center Cancer Biology program |
DOI:10.5524/100360 | Free, Available for download | biotools:vadir | ftp://penguin.genomics.cn/pub/10.5524/100001_101000/100360/, https://bio.tools/vadir | SCR_015797 | VaDiR: an integrated approach to Variant Detection in RNA | 2026-08-06 09:28:44 | 13 | ||||
|
Poretools Resource Report Resource Website 50+ mentions |
Poretools (RRID:SCR_015879) | sequence analysis software, software resource, data analysis software, software toolkit, data processing software, software application | Software toolkit for analyzing nanopore sequence data. | nanopore, sequence, python, oxford nanopore, MinION, quality control, downstream analysis, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: SoftCite |
Medical Research Council ; NHGRI R01 HG006693 |
PMID:25143291 | Open source, Free, Available for download | biotools:poretools | https://bio.tools/poretools | SCR_015879 | 2026-08-06 09:28:45 | 81 | ||||||
|
SwissTree Resource Report Resource Website 1+ mentions |
SwissTree (RRID:SCR_015881) | storage service resource, data set, project portal, service resource, data repository, data or information resource, portal | Project that aims to provide a collection of Gold Standard gene phylogenies to the scientific community. This set of reference gene trees is suitable for phylogenomic databases to assess their current quality status, measure changes following new database releases and diagnose improvements subsequent to an upgrade of the analysis procedure. | gene phylogeny, gene collection, gold standard, phylogenomic, database, genome analysis, bio.tools |
is listed by: bio.tools is listed by: Debian |
Swiss State Secretariat for Education ; Research and Innovation (SERI) ; Swiss National Science Foundation 150654 |
Public, Free, Available for download | biotools:swisstree | https://bio.tools/swisstree | SCR_015881 | 2026-08-06 09:28:45 | 3 | |||||||
|
PhyD3 Resource Report Resource Website 10+ mentions |
PhyD3 (RRID:SCR_015892) | PhyD3 | software resource, web application, data processing software, data visualization software, software application | Web application that is a phylogenetic tree viewer based on d3.js. It was developed as an alternative to Archaeopteryx inspired by d3.phylogram.js. | javascript, visualization, toolkit, phylogeny, program, phylogenetic data, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:28525531 | Open source, Demo available | biotools:phyd3 | https://github.com/vibbits/phyd3, https://bio.tools/phyd3 | SCR_015892 | 2026-08-06 09:28:45 | 47 | ||||||
|
TFBS Resource Report Resource Website 10+ mentions |
TFBS (RRID:SCR_015774) | data analysis software, software application, software resource, data processing software | Perl software for transcription factor binding site detection and analysis. It implements classes for the representation of objects encountered in analysis of these protein-binding sites. | protein-binding, transcription factor, factor binding, binding site detection, transcription analysis, perl, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
PMID:12176838 DOI:10.1093/bioinformatics/18.8.1135 |
Free, Available for download, No longer in development | biotools:tfbs, OMICS_20526 | https://github.com/ComputationalRegulatoryGenomicsICL/TFBS, https://bio.tools/tfbs, https://sources.debian.org/src/libtfbs-perl/ | SCR_015774 | 2026-08-06 09:28:42 | 44 | |||||||
|
Nanopolish Resource Report Resource Website 100+ mentions |
Nanopolish (RRID:SCR_016157) | data analysis software, software application, software resource, data processing software | Software package for signal-level analysis of Oxford Nanopore sequencing data. | Signal level analysis, Oxford Nanopore, sequencing data, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
Free, Available for download, Freely available | OMICS_16545, biotools:nanopolish | https://bio.tools/nanopolish, https://sources.debian.org/src/nanopolish/ | SCR_016157 | 2026-08-06 09:28:46 | 426 | ||||||||
|
DIAMOND Resource Report Resource Website 100+ mentions |
DIAMOND (RRID:SCR_016071) | sequence analysis software, software resource, data analysis software, data processing software, software application | Software that performs sequence alignment for protein and translated DNA searches and functions. Used for high performance analysis of big sequence data, protein-protein search, and DNA-protein search. | sequence, aligner, high, performance, analysis, big, data, protein, DNA, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools has parent organization: University of Tubingen; Tubingen; Germany |
PMID:25402007 DOI:10.1038/nmeth.3176 |
Free, Available for download | OMICS_08011, biotools:diamond | https://bio.tools/diamond, https://sources.debian.org/src/diamond-aligner/ | SCR_016071 | 2026-08-06 09:28:47 | 386 | |||||||
|
IDEPI - IDentify EPItopes Resource Report Resource Website |
IDEPI - IDentify EPItopes (RRID:SCR_016171) | software library, software toolkit, software resource | IDEPI is a domain-specific and extensible software library for supervised learning of models that relate genotype to phenotype for HIV-1 and other organisms. IDEPI makes use of open source libraries for machine learning (scikit- learn, scikit-learn.org/), sequence alignment (HMMER, hmmer.janelia.org/), sequence manipulation (BioPython, biopython.org), and parallelization (joblib, pythonhosted.org/joblib), and provides a programming interface to allow the users to engineer sequence features and select machine learning algorithms appropriate for their application. | modeling, machine, learning, bio.tools |
is listed by: Debian is listed by: bio.tools |
PMID:25254639 | Free, Available for download | biotools:idepi | https://bio.tools/idepi | SCR_016171 | 2026-08-06 09:28:49 | 0 | |||||||
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Genome Annotation Generator Resource Report Resource Website 10+ mentions |
Genome Annotation Generator (RRID:SCR_016053) | GAG | source code, sequence analysis software, software resource, data analysis software, data processing software, software application | Command line program to read, modify, annotate and generate genomic data. Can write files to .gff3 or to the NCBI's .tbl format. | genome, annotation, tbl, ncbi, command, line, code, modify, read, annotate, gff3, bio.tools |
is listed by: bio.tools is listed by: Debian |
Free, Available for download | biotools:gag | https://bio.tools/gag | SCR_016053 | gag.py | 2026-08-06 09:28:49 | 17 |
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