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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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python-biom-format Resource Report Resource Website 1+ mentions |
python-biom-format (RRID:SCR_024193) | software resource, source code | Software provides command line interface and Python API for working with Biological Observation Matrix files. | command line interface, Python API for working with Biological Observation Matrix files, BIOM files, |
is listed by: Debian is related to: biomformat |
PMID:23587224 | Free, Available for download, Freely available, | https://sources.debian.org/src/python3-biom-format/ | SCR_024193 | 2026-08-03 09:38:38 | 1 | ||||||||
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AETIONOMY Resource Report Resource Website 1+ mentions |
AETIONOMY (RRID:SCR_000232) | AETIONOMY | portal, organization portal, data or information resource, consortium | Consortium founded to establish mechanism-based taxonomies for Alzheimer's and Parkinson's disease and other neurodegenerative disorders (NDD), with the goal of facilitating development of more effective and targeted treatments. To do this, the consortium collects and analyzes data to: * Create new ways to combine underutilized data currently available in the literature, public databases, and from private companies * Determine how to dynamically organize and structure different types of knowledge about NDD * Determine how to apply this knowledge to construct new patient group classification * Identify correlations between disease features at molecular, tissue or organ-specific, and clinical levels * Identify sub-groups of patients based on the molecular cause of their disease, as opposed to the nature and location of their symptoms * Deliver data, tools, and recommendations for the biomedical community in the treatment of NDD A mechanism-based taxonomy is hoped to advance the: # Description and organization of the indication-specific data # Linking of data to disease models, based on causal and correlative relationships The expected outcome of AETIONOMY is a new NDD taxonomy system that distinguishes mixed pathologies, allowing for new features or classes to be added into the taxonomy, all with the goal of aiding drug and biomarker discovery. | drug development, drug, taxonomy, biomarker, etiology, epidemiology, neuroimaging, mechanism, clinical, clinical trial, database, classification, biological pathway, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Fraunhofer Institute for Algorithms and Scientific Computing SCAI; North Rhine-Westphalia; Germany |
IMI ; EFPIA |
nlx_157972, biotools:AETIONOMY | https://bio.tools/AETIONOMY | SCR_000232 | 2026-08-04 09:40:05 | 3 | |||||||
|
RSEM Resource Report Resource Website 50+ mentions |
RSEM (RRID:SCR_000262) | data processing software, software application, software resource, data analysis software | Software package for quantifying gene and isoform abundances from single end or paired end RNA Seq data. Accurate transcript quantification from RNA Seq data with or without reference genome. Used for accurate quantification of gene and isoform expression from RNA-Seq data. | quantifying, gene, isoform, abundance, single, end, paired, RNA seq, data, transcript, reference, genome, bio.tools |
is listed by: OMICtools is listed by: GitHub is listed by: bio.tools is listed by: Debian has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
PMID:21816040 | Free, Available for download, Freely available | OMICS_01966, OMICS_01287, biotools:rsem, SCR_013027 | https://github.com/deweylab/RSEM, https://github.com/deweylab/RSEM/releases, https://bio.tools/rsem, https://sources.debian.org/src/rsem/ | SCR_000262 | RSEM, RNA-Seq by Expectation-Maximization, RSEM-v1.3.0 | 2026-08-04 09:40:05 | 94 | ||||||
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PSCBS Resource Report Resource Website |
PSCBS (RRID:SCR_000417) | data processing software, data analysis software, software resource, sequence analysis software, software application | Software R package for segmentation of allele-specific DNA copy number data and detection of regions with abnormal copy number within each parental chromosome. Both tumor-normal paired and tumor-only analyses are supported. | abnormal copy number regions detection, allele specific DNA copy number data segmentation, |
is listed by: OMICtools is listed by: Debian is related to: CRAN has parent organization: University of California at San Francisco; California; USA |
PMID:21666266 DOI:10.1093/bioinformatics/btr329 |
Free, Available for download, Freely available | OMICS_05545 | https://sources.debian.org/src/r-cran-pscbs/ | SCR_000417 | PSCBS: Analysis of Parent-Specific DNA Copy Numbers | 2026-08-04 09:40:07 | 0 | ||||||
|
DESeq Resource Report Resource Website 100+ mentions |
DESeq (RRID:SCR_000154) | DESeq | data processing software, software application, software resource, data analysis software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 30,2023. Software for differential gene expression analysis based on the negative binomial distribution. It estimates variance-mean dependence in count data from high-throughput sequencing assays and tests for differential expression. | gene expression, binomial, differential, negative binomial distribution, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is hosted by: Bioconductor |
PMID:20979621 DOI:10.1186/s13059-014-0550-8 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01306, biotools:deseq | https://bio.tools/deseq, https://sources.debian.org/src/r-bioc-deseq2/ | SCR_000154 | 2026-08-04 09:40:04 | 473 | ||||||
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GASV Resource Report Resource Website 1+ mentions |
GASV (RRID:SCR_000061) | GASV | data processing software, software application, software resource, data analysis software | Software tool for identifying structural variants (SVs) from paired-end sequencing data.GASV distribution includes three components that are typically run in succession: the BAM file of unique paired-read mappings is processed; structural variants are identified by clustering discordant fragments; and a probabilistic algorithm improves the specificity of GASV predictions. | paired-end sequencing data, structural variant, probabilistic algorithm, discordant fragment, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is related to: GASVPro has parent organization: Brown University; Rhode Island; USA |
Burroughs Wellcome Fund ; Department of Defense Breast Cancer Research ; ADVANCE Program at Brown University ; NSF 0548311 |
PMID:19477992 | Free, Available for download, Freely available | biotools:gasv, OMICS_01352 | http://compbio.cs.brown.edu/projects/gasv/, https://bio.tools/gasv | SCR_000061 | Geometric Analysis of Structural Variants | 2026-08-04 09:40:03 | 4 | ||||
|
seq-annot Resource Report Resource Website 1+ mentions |
seq-annot (RRID:SCR_018731) | software application, software resource, software toolkit, standalone software | Software Python package for annotating and counting genomic features in genomes and metagenomes. Software tools to facilitate annotation and comparison of genomes and metagenomes. | Annotating, counting, comparison, genomic feature, genome, metagenome, metagenomics, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:seq-annot | https://bio.tools/seq-annot | SCR_018731 | 2026-08-04 09:44:27 | 1 | ||||||||
|
CiLiQuant Resource Report Resource Website |
CiLiQuant (RRID:SCR_019319) | data processing software, software application, software resource | Software tool to separate junction reads based on their linear or circular origin. Only non ambiguous junction reads are used to compare relative linear and circular transcript abundance. | RNA, splicing, circular origin, separate junction reads, circular transcript abundance, linear transcript abundance, compare, bio.tools |
is listed by: bio.tools is listed by: Debian |
FWO ; Special Research Fund UGent ; Stichting Tegen Kanker ; Kom Op Tegen Kanker (Stand Up To Cancer) ; European Union's Horizon 2020 |
Free, Available for download, Freely available | biotools:ciliquant | https://bio.tools/ciliquant | SCR_019319 | 2026-08-04 09:44:33 | 0 | |||||||
|
QuPath Resource Report Resource Website 1000+ mentions |
QuPath (RRID:SCR_018257) | data processing software, software application, software resource, image analysis software | Open Source software package for digital pathology image analysis. Used for whole slide image analysis and digital pathology. Provides researchers with batch processing and scripting functionality, and extensible platform with which to develop and share new algorithms to analyze complex tissue images. | Digital pathology, image analysis, whole slide image, batch processing, tissue image, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Queens University Belfast; Ireland; United Kingdom |
Invest Northern Ireland ; Experimental Cancer Medicine Centre Network ; Sean Crummey Memorial Fund ; Tom Simms Memorial Fund ; Friends of the Cancer Centre ; Cancer Research UK Accelerator |
PMID:29203879 | Free, Available for download, Freely available | biotools:qupath | https://bio.tools/qupath | SCR_018257 | 2026-08-04 09:44:22 | 1590 | ||||||
|
Bio-EUtilities Resource Report Resource Website |
Bio-EUtilities (RRID:SCR_024064) | software resource, software toolkit | Software package which interacts with and retrieves data from NCBI's eUtils. This distribution encompasses low-level API for interacting with (and storing) information from NCBI's eUtils interface. See Bio::DB::EUtilities for the query API to retrieve data from NCBI, and Bio::Tools::EUtilities for the general class storage system. Note this may change to utilize the XML schema for each class at some point, though we will attempt to retain current functionality for backward compatibility unless this becomes problematic. | interacting, storing information, NCBI's eUtils interface, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-eutilities-perl/ | SCR_024064 | Bio-EUtilities - BioPerl low-level API for retrieving and storing data from NCBI eUtils, libbio-eutilities-perl | 2026-08-04 09:45:25 | 0 | ||||||||
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Bio-Tools-Run-Alignment-Clustalw Resource Report Resource Website |
Bio-Tools-Run-Alignment-Clustalw (RRID:SCR_024067) | software resource, software toolkit | Software package for performing multiple sequence alignment from set of unaligned sequences and/or sub-alignments by means of the clustalw program. | performing multiple sequence alignment, set of unaligned sequences, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-tools-run-alignment-clustalw-perl/ | SCR_024067 | libbio-tools-run-alignment-clustalw-perl, Bio-Tools-Run-Alignment-Clustalw - Object for the calculation of a multiple sequence alignment from a set of unaligned sequences or alignments using the Clustalw program | 2026-08-04 09:45:25 | 0 | ||||||||
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Bio-Tools-Phylo-PAML Resource Report Resource Website |
Bio-Tools-Phylo-PAML (RRID:SCR_024069) | software resource, software toolkit | Software package used to parse output from the PAML programs codeml, baseml, basemlg, codemlsites and yn00. You can use the Bio-Tools-Run-Phylo-PAML modules to actually run some of the PAML programs, but this module is only useful to parse the output. | parse output, PAML programs, codeml, baseml, basemlg, codemlsites, yn00. | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-tools-phylo-paml-perl/ | SCR_024069 | libbio-tools-phylo-paml-perl, Bio-Tools-Phylo-PAML - Parses output from the PAML programs codeml, baseml, codemlsites and yn00, basemlg | 2026-08-04 09:45:24 | 0 | ||||||||
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Bio-Graphics Resource Report Resource Website |
Bio-Graphics (RRID:SCR_024061) | software resource, software toolkit | Software package to generate GD images of Bio::Seq objects. | generate GD images of Bio::Seq objects, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/libbio-graphics-perl/ | SCR_024061 | Bio-Graphics - Generate GD images of Bio-Seq objects, libbio-graphics-perl | 2026-08-04 09:45:25 | 0 | ||||||||
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CLI for BioMAJ Resource Report Resource Website |
CLI for BioMAJ (RRID:SCR_023980) | software resource, software toolkit | Software package to use BioMAJ providing biomaj-cli. | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/biomaj3-cli/ | SCR_023980 | biomaj3-cli, biomaj-cli | 2026-08-04 09:45:23 | 0 | |||||||||
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BCALM 2 Resource Report Resource Website 1+ mentions |
BCALM 2 (RRID:SCR_023975) | software application, software resource, source code | Software tool for constructing compacted de Bruijn graph from sequencing data.Parallel algorithm that distributes the input based on minimizer hashing technique, allowing for good balance of memory usage throughout its execution. | constructing compacted de Bruijn graph, sequencing data, | is listed by: Debian | PMID:27307618 | Free, Available for download, Freely available | OMICS_12164 | https://sources.debian.org/src/bcalm/ | SCR_023975 | bcalm | 2026-08-04 09:45:22 | 3 | ||||||
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GCLib Resource Report Resource Website |
GCLib (RRID:SCR_024028) | software toolkit, software resource, software library | Software genomic C++ library of reusable code for bioinformatics projects.Provides core collection of data structures, trying to avoid unnecessary code dependencies of other heavy libraries, while minimizing build time. | reusable code for bioinformatics, | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/gclib/ | SCR_024028 | gclib, genome-code-lib | 2026-08-04 09:45:23 | 0 | ||||||||
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CAT and BAT Resource Report Resource Website 1+ mentions |
CAT and BAT (RRID:SCR_023988) | software resource, software toolkit | Software pipeline for taxonomic classification of contigs and metagenome-assembled genomes. Contig Annotation Tool and Bin Annotation Tool for the taxonomic classification of long DNA sequences and metagenome assembled genomes of both known and unknown microorganisms, as generated by contemporary metagenomics studies. | taxonomic classification, long DNA sequences, metagenome assembled genomes, known and unknown microorganisms, contemporary metagenomics studies, | is listed by: Debian | PMID:31640809 | Free, Available for download, Freely available | https://sources.debian.org/src/cat-bat/ | SCR_023988 | Bin Annotation Tool, Contig Annotation Tool, BAT, CAT, cat-bat, CAT/BAT | 2026-08-04 09:45:23 | 2 | |||||||
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CTDConverter Resource Report Resource Website |
CTDConverter (RRID:SCR_024007) | software toolkit, software resource, software library | Software Python scripts to convert CTD files into other formats such as Galaxy, CWL. | Python, scripts to convert CTD files, Galaxy format, CWL format | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/ctdconverter/ | SCR_024007 | ctdconverter | 2026-08-04 09:45:23 | 0 | ||||||||
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FreeImage Resource Report Resource Website 1+ mentions |
FreeImage (RRID:SCR_024022) | software toolkit, software resource, software library | Open Source software library for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications. | support graphics image formats, PNG, BMP, JPEG, TIFF | is listed by: Debian | Free, Available for download, Freely available | https://sources.debian.org/src/freeimage/ | SCR_024022 | freeimage | 2026-08-04 09:45:23 | 2 | ||||||||
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GenomeTester4 Resource Report Resource Website 1+ mentions |
GenomeTester4 (RRID:SCR_024026) | software resource, software toolkit | Software toolkit for performing set operations - union, intersection and complement on k-mer lists. | performing set operations on k-mer lists, | is listed by: Debian | PMID:26640690 | Free, Available for download, Freely available, | OMICS_02363w | https://sources.debian.org/src/genometester/ | SCR_024026 | genometester | 2026-08-04 09:45:24 | 4 |
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