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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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TransDecoder Resource Report Resource Website 1000+ mentions |
TransDecoder (RRID:SCR_017647) | standalone software, data processing software, software resource, software application | Software tool to identify candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to genome using Tophat and Cufflinks.Starts from FASTA or GFF file. Can scan and retain open reading frames (ORFs) for homology to known proteins by using BlastP or Pfam search and incorporate results into obtained selection. Predictions can then be visualized by using genome browser such as IGV. | Identify, candidate, coding, region, transcript, sequence, de novo, RNAseq, assembly, alignment, genome, open, reading, frame, homology, protein, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:transDecoder, OMICS_10852 | https://bio.tools/TransDecoder, https://sources.debian.org/src/transdecoder/, https://github.com/TransDecoder/TransDecoder/wiki | SCR_017647 | , Find Coding Regions Within Transcripts | 2026-08-12 10:51:48 | 1572 | |||||||
|
Apache Spark Resource Report Resource Website 10+ mentions |
Apache Spark (RRID:SCR_016557) | data processing software, data analytics software, software resource, software application | Software tool as a unified analytics engine for large scale data processing. An open source distributed general purpose cluster computing framework. | unified, analytics, engine, large, scale, data, processing |
is related to: VariantSpark is related to: spark-xml is related to: spark-xml-utils is related to: SparkFHE has parent organization: University of California at Berkeley; Berkeley; USA |
DOI:10.1145/2934664 | Free, Available for download, Freely available | SCR_016557 | 2026-08-12 10:51:32 | 43 | |||||||||
|
docker4seq Resource Report Resource Website 1+ mentions |
docker4seq (RRID:SCR_017006) | data processing software, software resource, software application | 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 | 2026-08-12 10:51:41 | 6 | ||||||||
|
LACHESIS Resource Report Resource Website 50+ mentions |
LACHESIS (RRID:SCR_017644) | data processing software, software resource, software application | Software tool for chromosome scale scaffolding of de novo genome assemblies based on chromatin interactions.Method exploits signal of genomic proximity in Hi-C datasets for ultra long range scaffolding of de novo genome assemblies. | Chromosome, scale, scaffolding, de novo, genome, assembly, chromatin, Hi-C, data, clustering, contig | NHGRI HG006283; National Science Foundation ; NHGRI T32 HG000035 |
PMID:24185095 | Free, Available for download, Freely available | SCR_017644 | Ligating Adjacent Chromatin Enables Scaffolding In Situ | 2026-08-12 10:51:48 | 70 | ||||||||
|
AfterQC Resource Report Resource Website 10+ mentions |
AfterQC (RRID:SCR_016390) | data processing software, software resource, software application | Software that performs automatic filtering, trimming, error removing, and quality control for fastq data. | fastq, qc, editing, filtering, trimming, dna, rna, seq, sequence, sequencing, poly, pair-end, python | PMID:28361673 | Free, Available for download | SCR_016390 | After QC | 2026-08-12 10:51:33 | 15 | |||||||||
|
Prophet Resource Report Resource Website 1+ mentions |
Prophet (RRID:SCR_017083) | data processing software, software resource, software application | Open source software package for producing forecasts for time series data that has multiple seasonality with linear or non linear growth. Implemented in R or Phyton. | data, science, forecast, time, series, multiple, seasonality, linear, non linear, growth, analysis | is listed by: CRAN | DOI:10.7287/peerj.preprints.3190v2 | Free, Available for download, Freely available | https://cran.r-project.org/web/packages/prophet/, https://pypi.org/project/fbprophet/ | SCR_017083 | Prophet Automatic Forecasting Procedure | 2026-08-12 10:51:36 | 3 | |||||||
|
WinRHIZO Resource Report Resource Website 10+ mentions |
WinRHIZO (RRID:SCR_017120) | data processing software, image analysis software, software resource, software application | Software toolbox for image analysis by Regent Instruments Inc. Used for root measurement in different forms like morphology, topology, architecture and color analyses. Automatically or interactively analyses washed roots. | image, analysis, root, measurement, plant, morphology, topology, color, Regent Instruments Inc. | Available for purchase | SCR_017120 | 2026-08-12 10:51:37 | 16 | |||||||||||
|
AIMLESS Resource Report Resource Website 500+ mentions |
AIMLESS (RRID:SCR_015747) | data processing software, software resource, software application | Data processing software for x-ray diffraction data. AIMLESS scales together multiple observations of reflections, and merges multiple observations into an average intensity. | xray, differentiation, observation, reflection, scaling, scale | has parent organization: MRC Laboratory of Molecular Biology | PMID:23793146 | Free, Available for download | SCR_015747 | 2026-08-12 10:51:22 | 571 | |||||||||
|
autoPROC Resource Report Resource Website 100+ mentions |
autoPROC (RRID:SCR_015748) | data processing software, software application, software toolkit, software resource | Data processing software for X-ray diffraction data. autoPROC is a set of tools and programs to automate steps involved in data processing, such as image analysis, integration, indexing, and determination. | xray, diffraction, data processing, crystallography | European Commission LSHG-CT-2003-503420 | PMID:21460447 | Free for academic use, Available for download | SCR_015748 | 2026-08-12 10:51:14 | 330 | |||||||||
|
atacr Resource Report Resource Website 1+ mentions |
atacr (RRID:SCR_016286) | data processing software, software resource, software application | Software that analyzes count data from RNA-capture-seq and ATAC-capture-seq experiments. Using BioConductor RangedSummarizedExperiment objects, atacr implements a set of helper functions and quality control plots specific to the analysis of counts of reads in windows across genomes. | normalization, bootstrap, bayes, factor, test, reference, design, seq, count, capture, data | Gatsby Charitable Foundation ; Marie Curie 656243 |
Free, Available for download, Tutorial available | SCR_016286 | 2026-08-12 10:51:23 | 2 | ||||||||||
|
Studylog Resource Report Resource Website 1+ mentions |
Studylog (RRID:SCR_016682) | data or information resource, portal, service resource, organization portal | Commerciall organization to develop study protocols collaboratively to run and manage animal research studies for academic, government, biotech and pharmaceutical labs. Provides services, including product installation and configuration, user training, customization services and ongoing support. | develop, study, protocol, collaborative, animal, research | SCR_016682 | 2026-08-12 10:51:29 | 5 | ||||||||||||
|
Slingshot Resource Report Resource Website 100+ mentions |
Slingshot (RRID:SCR_017012) | data processing software, software resource, software application | Software R package for identifying and characterizing continuous developmental trajectories in single cell data. Cell lineage and pseudotime inference for single-cell transcriptomics. | identify, characterize, continuous, developmental, trajectory, single, cell, data, lineage, pseudotime, inference, transcriptomic | is used by: Totem | NIMH U01 MH105979; NIDCD R01 DC007235; NCRR S10 RR029668; Siebel Foundation ; NIA K01 AG045344; NHGRI T32 HG000047; California Institute of Regenerative Medicine |
PMID:29914354 | Free, Available for download, Freely available | SCR_017012 | 2026-08-12 10:51:41 | 102 | ||||||||
|
imctools Resource Report Resource Website 10+ mentions Rating or validation data |
imctools (RRID:SCR_017132) | IMCtools | data processing software, software resource, software application | Software Python package that implements preprocessing pipeline for imaging mass cytometry data. Can convert IMC raw files to tiff files that are used as inputs into CellProfiller, Ilastik, Fiji etc. | preprocessing, pipeline, imaging, mass, cytometry, data, convert, IMC, raw, file, TIFF |
has parent organization: University of Zurich; Zurich; Switzerland is a plug in for: Fiji |
Swiss National Science Foundation ; SNSF Assistant Professorship grant ; PhosphonetPPM and MetastasiX SystemsX grant ; NIDDK UC4 DK108132; European Research Council ; Roche Postdoctoral Fellowship |
PMID:29605184 | Free, Available for download, Freely available | https://bodenmillergroup.github.io/imctools/build/html/index.html | SCR_017132 | imaging mass spectrometry tools | 2026-08-12 10:51:41 | 25 | |||||
|
Purge_haplotigs Resource Report Resource Website 10+ mentions |
Purge_haplotigs (RRID:SCR_017616) | data processing software, software resource, software application | Pipeline for reassigning primary contigs that should be labelled as haplotigs. Used for third generation sequencing based assemblies to automate reassignment of allelic contigs, and to assist in manual curation of genome assemblies. | Reassigning, primary, contig, label, haplotig, third, generation, sequencing, assembly, allelic, curation, genome, alignment | PMID:30497373 | Free, Available for download, Freely available | SCR_017616 | 2026-08-12 10:51:50 | 14 | ||||||||||
|
PsychENCODE Knowledge Portal Resource Report Resource Website 10+ mentions |
PsychENCODE Knowledge Portal (RRID:SCR_017500) | data or information resource, project portal, database, portal | Portal of PsychENCODE Consortium to study role of rare genetic variants involved in several psychiatric disorders. Database of regulatory elements, epigenetic modifications, RNA and protein in brain. | Rare, genetic, variant, psychiatric, disorder, regulatory, element, epigenetic, modification, RNA, protein, brain | Restricted | SCR_017500 | 2026-08-12 10:51:48 | 15 | |||||||||||
|
NMF Toolbox Resource Report Resource Website 1+ mentions |
NMF Toolbox (RRID:SCR_017069) | data processing software, software resource, software application | Software toolbox for performing Non-negative Matrix Factorization (NMF) and several variants. Used to factorize one non negative matrix into two non negative factors, that is basis matrix and coefficient matrix. Applied in bioinformatics as data mining approach. | non negative, matrix, factorization, variant, coefficient, data, mining, bioinformatics |
is related to: MATLAB is related to: Algorithms and Framework for Nonnegative Matrix Factorization has parent organization: University of Southern California; Los Angeles; USA |
Free, Available for download, Freely available | https://sites.google.com/site/nmftool/, https://sail.usc.edu/~cvaz/nmftoolbox.html | SCR_017069 | NMF MATLAB Toolbox, Non-negative Matrix Factorization toolbox, Non negative Matrix Factorization Toolbox, NMF Toolbox | 2026-08-12 10:51:40 | 4 | ||||||||
|
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 | data processing software, software resource, software application | 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 | 2026-08-12 10:51:50 | 2 | |||||
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Inxight Resource Report Resource Website 10+ mentions |
Inxight (RRID:SCR_016490) | data or information resource, database, portal, organization portal | Portal of NCATS (the National Center for Advancing Translational Sciences) for drug development information including:US approved drugs, marketed drugs, investigational drugs. Provides manually curated data supplied by the FDA and private companies. Provides drugs marketing and regulatory status, drug ingredient definitions, biological activity and clinical use. | drug, development, information, approved, marketed, investigational, data, supply, FDA, company, regulatory, status, ingredient, definition, biological, activity, clinical, use | NIH | Free, Freely available | SCR_016490 | 2026-08-12 10:51:26 | 16 | ||||||||||
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CAPT Resource Report Resource Website 1+ mentions |
CAPT (RRID:SCR_016305) | data processing software, image analysis software, software resource, software application | Software for molecular weight, quantification of bands, colony counting and distance calculation in Vilber Lourmat gel documentation imaging systems. Used in molecular biology laboratories. | gel, image, molecular, weight, quantification, band, colony, count, distance, calculation, imaging, system | Commercially available | SCR_016305 | 2026-08-12 10:51:32 | 4 | |||||||||||
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refine.bio Resource Report Resource Website 1+ mentions |
refine.bio (RRID:SCR_017471) | data processing software, software resource, software application | Software tool to uniformly process and normalize large amounts of data. Harmonizes petabytes of publicly available biological data into ready-to-use datasets for cancer researchers and AI/ML scientists. | Process, normalize, large, amount, data, cancer, dataset, standardized, pipeline, gene, expression | Free, Available for download, Freely available | https://www.refine.bio/ | SCR_017471 | 2026-08-12 10:51:48 | 1 |
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