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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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VMD Resource Report Resource Website 10+ mentions |
VMD (RRID:SCR_024368) | software application, software resource | Software tool as molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS X, Unix, or Windows, is distributed free of charge, and includes source code. | molecular visualization, displaying, animating, analyzing, large biomolecular systems, . | is listed by: Debian | Free, Available for download, Freely available, | https://sources.debian.org/src/vmd/ | SCR_024368 | vmd | 2026-07-26 09:08:24 | 33 | ||||||||
|
mirtop Resource Report Resource Website |
mirtop (RRID:SCR_024116) | software application, software resource | Command lines tool to annotate miRNAs with standard mirna/isomir naming. | annotate miRNAs, standard mirna/isomir naming, | is listed by: Debian | DOI:10.7490/f1000research.1115724.1 | Free, Available for download, Freely available, | OMICS_31718 | https://sources.debian.org/src/mirtop/, https://mirtop.readthedocs.io/en/latest/ | SCR_024116 | 2026-07-26 09:08:17 | 0 | |||||||
|
mPSQed Resource Report Resource Website |
mPSQed (RRID:SCR_024118) | software application, software resource | Software tool for the design of multiplex pyrosequencing assays. | design of multiplex pyrosequencing assays, | is listed by: Debian | PMID:22675516 | Free, Available for download, Freely available, | OMICS_33146 | https://sources.debian.org/src/mpsqed/ | SCR_024118 | mpsqed | 2026-07-26 09:08:20 | 0 | ||||||
|
SMILE Resource Report Resource Website 1+ mentions |
SMILE (RRID:SCR_024119) | software application, software resource | Software tool that infers motifs in set of sequences to infer exceptionnal sites as binding sites in DNA sequences. 1.4 version allows to infer motifs written on any alphabet in any kind of sequences. Allows to deal with motifs associated by some distance constraints. Used to group under unique model different occurrences composed of several boxes separated by spacers of different lengths. | infers motifs in set of sequences, binding sites in DNA sequences, distance constraints, | is listed by: Debian | Free, Available for download, Freely available, | OMICS_20188 | https://sources.debian.org/src/mlv-smile/ | SCR_024119 | mlv-smile | 2026-07-26 09:08:17 | 1 | |||||||
|
COILS: Prediction of Coiled Coil Regions in Proteins Resource Report Resource Website 100+ mentions |
COILS: Prediction of Coiled Coil Regions in Proteins (RRID:SCR_008440) | software application, software resource, data processing software | COILS is a program that compares a sequence to a database of known parallel two-stranded coiled-coils and derives a similarity score. By comparing this score to the distribution of scores in globular and coiled-coil proteins, the program then calculates the probability that the sequence will adopt a coiled-coil conformation. | software, prediction, database, sequence, coil, globular, protein, probability, bio.tools, FASEB list |
is listed by: 3DVC is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
DOI:10.1126/science.252.5009.1162 | biotools:ncoils, OMICS_07850, nif-0000-30263 | https://bio.tools/ncoils, https://sources.debian.org/src/ncoils/ | https://sources.debian.org/src/ncoils/ | SCR_008440 | COILS Server | 2026-07-26 09:04:39 | 164 | ||||||
|
SeqExpress Resource Report Resource Website |
SeqExpress (RRID:SCR_007075) | software application, software resource, data processing software | A comprehensive analysis and visualization software package for gene expression experiments that provides: a number of clustering and analysis techniques; integrated gene expression and analysis result visualizations, integration with the Gene Expression Omnibus; and an optional data sharing architecture. GO is used to assign functional enrichment scores to clusters, using a combination of specially developed techniques and general statistical methods. These results can be explored using the in built ontology browsing tool or through the generated web pages. SeqExpress also supports numerous data transformation, projection, visualization, file export/import, searching, integration (with R), and clustering options. | gene, gene expression, function, analysis, visualization, statistical analysis, windows, c#, gene function, chromosome location, bio.tools |
is listed by: Gene Ontology Tools is listed by: bio.tools is listed by: Debian is related to: Gene Ontology is related to: Gene Expression Omnibus |
PMID:14988116 | Free | nlx_149285, biotools:seqexpress | https://bio.tools/seqexpress | SCR_007075 | 2026-07-26 09:04:28 | 0 | |||||||
|
epigenomix Resource Report Resource Website 1+ mentions |
epigenomix (RRID:SCR_006407) | epigenomix | software application, software resource, data processing software | Software package for the integrative analysis of microarray based gene expression and histone modification data obtained by ChIP-seq. The package provides methods for data preprocessing and matching as well as methods for fitting bayesian mixture models in order to detect genes with differences in both data types. | epigenetic, gene expression, microarray, histone modification, chip-seq, classification, differential expression, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:24403540 | GNU Lesser General Public License, v3 | biotools:epigenomix, OMICS_02205 | https://bio.tools/epigenomix | SCR_006407 | epigenomix - Epigenetic and gene expression data normalization and integration with mixture models | 2026-07-26 09:04:16 | 2 | |||||
|
SOAPaligner/soap2 Resource Report Resource Website 100+ mentions |
SOAPaligner/soap2 (RRID:SCR_005503) | SOAPaligner, SOAP2 | software application, software resource, data processing software | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 12,2024. Updated version of SOAP software for short oligonucleotide alignment that features in super fast and accurate alignment for huge amounts of short reads generated by Illumina/Solexa Genome Analyzer., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | next generation sequencing, alignment, short read, oligonucleotide, single-read, pair-end, resequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SOAP |
PMID:19497933 DOI:10.1093/bioinformatics/btn025 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:soap2 | https://bio.tools/soap2, https://sources.debian.org/src/soapaligner/ | SCR_005503 | 2026-07-26 09:03:57 | 322 | ||||||
|
Subread Resource Report Resource Website 1000+ mentions |
Subread (RRID:SCR_009803) | software application, software resource, data processing software | Software package for high-performance read alignment, quantification and mutation discovery.General purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. Subread aligner as fast, accurate and scalable read mapping by seed-and-vote.These programs were also implemented in Bioconductor R package Rsubread. | read alignment, DNA-seq reads mapping, RNA-seq reads mapping, mutation discovery, , bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Rsubread has parent organization: University of Melbourne; Victoria; Australia |
Australian National Health and Medical Research Council ; Victorian State Government Operational Infrastructure Support ; Australian Government |
PMID:23558742 | Free, Freely available | OMICS_01255, biotools:subread | https://bio.tools/subread, https://sources.debian.org/src/subread/ | SCR_009803 | 2026-07-26 09:05:12 | 1854 | ||||||
|
GSA-SNP Resource Report Resource Website 10+ mentions |
GSA-SNP (RRID:SCR_013109) | GSA-SNP | software application, software resource, data processing software | A tool for the gene-set (or pathway) analysis of a genome-wide association study result. It accepts a genome-wide list of SNPs and their association P-values. It summarizes the SNP P-values into nearby genes. The gene-by-gene summary results are then further summarized by gene-sets such as Gene Ontology, KEGG pathways, or user-created gene-sets. Various standardization and statistical tests can be performed and the resulting gene-sets that pass a significance level after multiple-testing correction are reported. The tool is written in Java and is available as a standalone version. | clinical neuroinformatics, computational neuroscience, imaging genomics, bio.tools |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is listed by: Debian is listed by: bio.tools has parent organization: Soongsil University; Seoul; South Korea |
PMID:20501604 | GNU General Public License v2 | nlx_155765, biotools:gsa-snp | https://bio.tools/gsa-snp | SCR_013109 | 2026-07-26 09:05:49 | 18 | ||||||
|
Trim Galore Resource Report Resource Website 5000+ mentions Rating or validation data |
Trim Galore (RRID:SCR_011847) | Trim Galore! | software application, software resource, data processing software | Software tool to automate quality and adapter trimming as well as quality control, with some added functionality to remove biased methylation positions for RRBS sequence files for directional, non-directional or paired-end sequencing. Wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for Reduced Representation Bisulfite Sequencing data. | Automate, quality, adapter, trimming, remove, biased, methylation, position, RRBS, reduced, representation, bisulfite, data, sequence, wrapper, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Babraham Institute works with: cutadapt |
Free, Available for download, Freely available | biotools:trim_galore, OMICS_01096, SCR_016946 | https://github.com/FelixKrueger/TrimGalore, https://bio.tools/trim_galore, https://sources.debian.org/src/trim-galore/ | SCR_011847 | TrimGalore | 2026-07-26 09:05:32 | 6255 | ||||||
|
docker4seq Resource Report Resource Website 1+ mentions |
docker4seq (RRID:SCR_017006) | software application, software resource, data processing software | Software R package to execute next generation sequencing computing applications, e.g. reads mapping and counting, wrapped in docker containers. | next, generation, sequencing, computing, application, read, mapping, count, docker, container, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: University of Turin;Turin;Italy |
Free, Available for download, Freely available | biotools:docker4seq | https://kendomaniac.github.io/docker4seq/index.html, https://bio.tools/docker4seq | SCR_017006 | 2026-07-26 09:06:54 | 5 | ||||||||
|
ProCon - PROteomics CONversion Resource Report Resource Website 1+ mentions |
ProCon - PROteomics CONversion (RRID:SCR_016363) | ProCon | software application, software resource, data processing software | Java based conversion tool for conversion of data from Proteomics files or a LIMS (Laboratory Information Management System) database into standard formats. Used to support wet-lab scientists in creating proteomics data files ready for upload into the public repositories. | data, proteomics, conversion, file, laboratory, information, management, system, database, standard, format, , bio.tools |
is listed by: Debian is listed by: bio.tools is related to: Ruhr University Bochum; North Rhine-Westphalia; Germany |
European Union Projects ProDac ; European Union Projects ProteomeXchange ; the German Federal Ministry of Education and Research BMBF |
PMID:26182917 | Free, Available for download, Freely available | biotools:procon | https://bio.tools/procon | SCR_016363 | PROteomics CONversion | 2026-07-26 09:06:43 | 1 | ||||
|
NanoFilt Resource Report Resource Website 100+ mentions |
NanoFilt (RRID:SCR_016966) | software application, software resource, data processing software | Software tool written in Python to perform its filtering based on mean read quality and GC content and read length. Used for filtering and trimming of long read sequencing data. | filtering, trimming, long, sequencing, data, read |
is listed by: OMICtools is listed by: Debian |
Free, Available for download, Freely available | https://sources.debian.org/src/nanofilt/ | SCR_016966 | 2026-07-26 09:06:51 | 268 | |||||||||
|
ScaffMatch Resource Report Resource Website 1+ mentions |
ScaffMatch (RRID:SCR_017025) | software application, software resource, data processing software | Software tool as scaffolding algorithm based on maximum weight matching able to produce high quality scaffolds from next generation sequencing data (reads and contigs). Able to handle reads with both short and long insert sizes. | scaffolding, algorithm, maximum, weight, matching, next, generation, sequencing, data, read, contig, bio.tools |
uses: Python Programming Language is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Georgia State University; Georgia; USA |
NSF IIS 0916401 | PMID:25890305 | Free, Available for download, Freely available | biotools:scaffmatch, OMICS_08198 | http://alan.cs.gsu.edu/NGS/?q=content/scaffmatch, https://bio.tools/scaffmatch | SCR_017025 | 2026-07-26 09:06:54 | 1 | ||||||
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Racon Resource Report Resource Website 100+ mentions |
Racon (RRID:SCR_017642) | software application, software resource, data processing software | Software tool as de novo genome assembly from long uncorrected reads. Used to correct raw contigs generated by rapid assembly methods which do not include consensus step. Supports data produced by Pacific Biosciences and Oxford Nanopore Technologies. | Assembly, de novo, long, uncorrected, read, raw, contig, consensus, step, data, sequence, bio.tools |
is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
Croatian Science Foundation ; Croatian Academy of Sciences and Arts ; A*STAR ; Singapore |
DOI:10.1101/068122 | Free, Available for download, Freely available | OMICS_25714, biotools:Racon, BioTools:Racon | https://bio.tools/Racon, https://sources.debian.org/src/racon/ | SCR_017642 | 2026-07-26 09:07:03 | 149 | ||||||
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CiLiQuant Resource Report Resource Website |
CiLiQuant (RRID:SCR_019319) | software application, software resource, data processing software | 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 | 2026-07-26 09:07:34 | 0 | |||||||
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Recognition of Errors in Assemblies using Paired Reads Resource Report Resource Website 1+ mentions |
Recognition of Errors in Assemblies using Paired Reads (RRID:SCR_017625) | REAPR | software application, software resource, data processing software | Software tool to identify errors in genome assemblies without need for reference sequence. Can be used in any stage of assembly pipeline to automatically break incorrect scaffolds and flag other errors in assembly for manual inspection. Reports mis-assemblies and other warnings, and produces new broken assembly based on error calls. | Identify, error, genome, assembly, without, reference, sequence, incorrect, scaffold, error |
is listed by: Debian is listed by: OMICtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
European Union ; Wellcome Trust ; JSPS KAKENHI |
PMID:23710727 | Free, Available for download, Freely available | OMICS_04068 | https://sources.debian.org/src/reapr/ | SCR_017625 | 2026-07-26 09:07:02 | 2 | |||||
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FlowCal Resource Report Resource Website 1+ mentions |
FlowCal (RRID:SCR_018140) | software application, software resource, data processing software | Open source software tool for automatically converting flow cytometry data from arbitrary to calibrated units. Can be run using intuitive Microsoft Excel interface, or customizable Python scripts. Software accepts Flow Cytometry Standard (FCS) files as inputs and is compatible with different calibration particles, fluorescent probes, and cell types. Automatically gates data, calculates common statistics, and produces plots. | Converting flow cytometry data, arbitrary unit, calibrated unit, data gating, statistic, plot, data, bio.tools |
is listed by: Debian is listed by: bio.tools |
NSF EFRI 1137266; NSF MCB 1244135; Office of Naval Research MURI N000141310074; Office of Naval Research YIP N000141410487; NIAID R21 AI115014; Welch Foundation ; NSF Graduate Research Fellowship DGE 0940902; NDSEG Fellowship |
PMID:27110723 | Free, Available for download, Freely available | biotools:flowcal | https://bio.tools/flowcal | SCR_018140 | Python Flow Cytometry Calibration Library | 2026-07-26 09:07:12 | 5 | |||||
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halSynteny Resource Report Resource Website 1+ mentions |
halSynteny (RRID:SCR_018127) | software application, software resource, data processing software | Software tool as conserved synteny block construction method for multiple whole-genome alignments. Implementation of DAG-based for reconstruction of synteny blocks from genome alignment. | Conserved synteny, block construction method, genome alignment, DAG based reconstruction, synteny block, chromosome, bio.tools |
is listed by: Debian is listed by: bio.tools |
Free, Freely available | biotools:halSynteny | https://bio.tools/halSynteny | SCR_018127 | Hierarchical Alignment Format Synteny | 2026-07-26 09:07:12 | 3 |
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