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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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DESeq2 Resource Report Resource Website 10000+ mentions |
DESeq2 (RRID:SCR_015687) | software application, data processing software, software tool, data analysis software, software resource | Software package for differential gene expression analysis based on the negative binomial distribution. Used for analyzing RNA-seq data for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. | differential, gene, expression, analysis, binominal, distribution, RNA-seq data, Bioconductor, bio.tools |
is used by: Glimma is used by: TEtranscripts is listed by: Bioconductor is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: SARTools works with: tximport |
International Max Planck Research School for Computational Biology and Scientific Computing ; NCI T32 CA009337; European Union’s 7th Framework Programme |
Free, Available for download, Freely available | biotools:deseq2 | https://github.com/mikelove/DESeq2 https://bio.tools/deseq2 |
SCR_015687 | 2026-02-17 10:02:36 | 43994 | |||||||
|
Pipeline Pilot Resource Report Resource Website 100+ mentions |
Pipeline Pilot (RRID:SCR_014917) | data analysis software, software application, data processing software, software resource | Software used to automate the process of accessing, analyzing and reporting scientific data. This software can be used by a person with little or no software development experience can create scientific protocols that can be executed through a variety of interfaces including: BIOVIA Web Port, other BIOVIA solutions such as BIOVIA Electronic Lab Notebook, Isentris, Chemical Registration and third-party applications such as Microsoft SharePoint. The protocols aggregate and provide immediate access to volumes of research data, they automate the scientific analysis of data and allow researchers to explore, visualize and report results. | automation, accessing, analysis, analyzing, scientific data, aggregation. aggregate, research, scientific | is listed by: SoftCite | Commercial | SCR_014917 | 2026-02-17 10:02:57 | 352 | ||||||||||
|
RepeatModeler Resource Report Resource Website 1000+ mentions |
RepeatModeler (RRID:SCR_015027) | software application, data processing software, data analysis software, software resource, sequence analysis software | Sequence analysis software that performs repeat family identification and creates models for sequence data. RepeatModeler utilizes RepeatScout and RECON to identify repeat element boundaries and family relationships., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | sequence analysis, sequence repeats, repeat identification, bio.tools |
uses: RepeatScout is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: Dfam |
Institute for Systems Biology ; NHGRI R44 HG02244; NHGRI R01 HG002939 |
THIS RESOURCE IS NO LONGER IN SERVICE | biotools:repeatmodeler | https://bio.tools/repeatmodeler | SCR_015027 | 2026-02-17 10:02:22 | 3193 | |||||||
|
pheatmap Resource Report Resource Website 1000+ mentions |
pheatmap (RRID:SCR_016418) | pheatmap | software application, data processing software, data acquisition software, image acquisition software, software resource, software toolkit | Software tool as a function in R to draw clustered heatmaps for better control over graphical parameters. | draw, clustered, heatmap, control, graphical, parameter, size, shape, text, bio.tools |
is used by: ClustVis is listed by: Debian is listed by: bio.tools is listed by: OMICtools is listed by: SoftCite is related to: CRAN |
Free, Available for download, Freely available | biotools:pheatmap, OMICS_26726 | https://github.com/raivokolde/pheatmap https://cran.r-project.org/web/packages/pheatmap/pheatmap.pdf https://bio.tools/pheatmap https://sources.debian.org/src/r-cran-pheatmap/ |
SCR_016418 | pretty heatmap | 2026-02-17 10:02:42 | 1068 | ||||||
|
SRAMP Resource Report Resource Website 100+ mentions |
SRAMP (RRID:SCR_024500) | simulation software, software application, software resource | Software tool as computational predictor of mammalian m(6)A site. Used for prediction of mammalian N6-methyladenosine (m6A) sites based on sequence-derived features. | mammalian m(6)A site predictor, sequence derived features based predictor, | is listed by: SoftCite | PMID:26896799 | Free, Available for download, Freely available | SCR_024500 | Sequence-based Rna Adenosine Methylation site Predictor | 2026-02-17 10:04:50 | 269 | ||||||||
|
RNAfold Resource Report Resource Website 50+ mentions |
RNAfold (RRID:SCR_024427) | data access protocol, web service, software resource | Web server predict secondary structures of single stranded RNA or DNA sequences. | predict secondary structures, single stranded RNA, DNA sequences, | is listed by: SoftCite | Free, Freely available | SCR_024427 | 2026-02-17 10:04:09 | 51 | ||||||||||
|
Nano Measurer Resource Report Resource Website 1+ mentions |
Nano Measurer (RRID:SCR_024493) | data analysis software, software application, data processing software, software resource | Software tool to process micrograph images for particle size. | process micrograph images, images for particle size, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024493 | 2026-02-17 10:04:50 | 4 | ||||||||||
|
ToposPro Resource Report Resource Website 10+ mentions |
ToposPro (RRID:SCR_024496) | data analysis software, software application, data processing software, software resource | Software package for analysis of geometrical and topological properties of periodic structures including crystals, networks, tilings.ToposPro was tailored to process large samples of crystallographic data and to find correlations between structure parameters. | geometrical and topological properties analysis, crystals, networks, tilings, periodic structures analysis, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024496 | 2026-02-17 10:04:10 | 14 | ||||||||||
|
Stem Resource Report Resource Website 1+ mentions |
Stem (RRID:SCR_024499) | data analysis software, software application, data processing software, software resource | Software tool for analysis of short time series gene expression data. Java program for clustering, comparing, and visualizing short time series gene expression data from microarray experiments. Allows to identify significant temporal expression profiles and genes associated with these profiles and to compare behavior of these genes across multiple conditions. STEM is fully integrated with the Gene Ontology. | short time series gene expression data analysis, clustering, comparing, visualizing, short time series gene expression data, microarray experiments data, identify temporal expression profiles identify genes associated with expression profiles, compare behavior of genes across multiple conditions, | is listed by: SoftCite | PMID:16597342 | Free, Available for download, Freely available | SCR_024499 | Short Time-series Expression Miner | 2026-02-17 10:04:10 | 5 | ||||||||
|
lDDT Resource Report Resource Website 1+ mentions |
lDDT (RRID:SCR_024524) | data access protocol, web service, software resource | Web server for local superposition free score for comparing protein structures and models using distance difference tests. Superposition free score that evaluates local distance differences of all atoms in model, including validation of stereochemical plausibility. | local superposition free score, comparing protein structures and models, distance difference tests, | is listed by: SoftCite | PMID:23986568 | Free, Freely available | SCR_024524 | Local Distance Difference Test | 2026-02-17 10:04:50 | 1 | ||||||||
|
RNALocate Resource Report Resource Website 10+ mentions |
RNALocate (RRID:SCR_024418) | data access protocol, web service, software resource | Web tool for RNA subcellular localizations analysis. RNALocate v2.0 is updated resource for RNA subcellular localization with increased coverage and annotation. | RNA subcellular localizations analysis, | is listed by: SoftCite | Scientific Research Fund of Heilongjiang Provincial Education Department ; National Key Research and Development Project of China ; National Natural Science Foundation of China ; Paul K. and Diane Shumaker Endowment Fund at University of Missouri ; Guangdong Basic and Applied Basic Research Foundation |
PMID:27543076 PMID:34551440 |
Free, Freely available | http://www.rna-society.org/rnalocate/ http://www.rnalocate.org/ |
SCR_024418 | RNALOCATE, RNALocate v2.0 | 2026-02-17 10:04:48 | 12 | ||||||
|
SimPhy Resource Report Resource Website 1+ mentions |
SimPhy (RRID:SCR_024501) | simulation software, software application, software resource | Software package for simulation of multiple gene families evolving under incomplete lineage sorting, gene duplication and loss, horizontal gene transfer, all three potentially leading to species tree/gene tree discordance and gene conversion. Used for phylogenomic simulation of gene, locus, and species trees. | phylogenomic simulation, gene phylogenomic simulation, locus phylogenomic simulation, species trees phylogenomic simulation, | is listed by: SoftCite | PMID:26526427 | Free, Available for download, Freely available | SCR_024501 | 2026-02-17 10:04:10 | 1 | |||||||||
|
CRISPResso2 Resource Report Resource Website 10+ mentions |
CRISPResso2 (RRID:SCR_024503) | data analysis software, software application, data processing software, software resource | Software pipeline designed to enable rapid and intuitive interpretation of genome editing experiments. Used for analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments. | sequencing data analysis, genome editing experiments interpretation, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024503 | 2026-02-17 10:04:50 | 44 | ||||||||||
|
OpenBUGS Resource Report Resource Website 100+ mentions |
OpenBUGS (RRID:SCR_024488) | data analysis software, software application, data processing software, software resource | Software for analysing complex statistical models using Markov chain Monte Carlo methods. | analysing complex statistical models, Markov chain Monte Carlo method, | is listed by: SoftCite | Free, Available for download, Freely available | SCR_024488 | Open Bayesian inference Using Gibbs Sampling | 2026-02-17 10:04:10 | 154 | |||||||||
|
AutoRT Resource Report Resource Website 1+ mentions |
AutoRT (RRID:SCR_024513) | simulation software, software application, software resource | Software tool for peptide retention time prediction using deep learning. Supports peptide retention prediction for tryptic peptides, MHC bound peptides and PTM peptides. | proteogenomics analysis | is listed by: SoftCite | PMID:32273506 | Free, Available for download, Freely available | SCR_024513 | 2026-02-17 10:04:10 | 2 | |||||||||
|
ModFOLD Resource Report Resource Website 1+ mentions |
ModFOLD (RRID:SCR_024518) | data access protocol, web service, software resource | Web server for the global and local quality estimation of 3D protein models | quality estimation, 3D protein models, | is listed by: SoftCite | PMID:28460136 | Restricted | SCR_024518 | ModFOLD6, ModFOLD8 | 2026-02-17 10:04:11 | 2 | ||||||||
|
ImageQuant Resource Report Resource Website 5000+ mentions |
ImageQuant (RRID:SCR_014246) | IQTL | image analysis software, software application, data processing software, software resource | Software for automatic general image analysis. It provides fully automatic analysis of 1-D gels including lane creation, background subtraction, band detection, molecular weight calibration, quantity calibration, and normalization. Editing tools are provided for cropping, rotating, and filtering images., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | automatic image analysis, general image analysis, image analysis software |
is listed by: SoftCite has parent organization: GE Healthcare |
THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014246 | ImageQuant TL | 2026-02-17 10:02:44 | 9230 | ||||||||
|
ImageScope Resource Report Resource Website 1000+ mentions |
ImageScope (RRID:SCR_014311) | image analysis software, software application, data processing software, software resource | Slide image modification software that allows the user to adjust the magnification, compare slides, pan and zoom, annotate specific areas, and perform image analysis of digital slides. Users can create macros and algorithms to automate analysis and create plots, respectively., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | slide image modification, viewing program |
is listed by: SoftCite has parent organization: University of Chicago; Illinois; USA |
THIS RESOURCE IS NO LONGER IN SERVICE | http://www.leicabiosystems.com/digital-pathology/digital-pathology-management/imagescope/ | SCR_014311 | 2026-02-17 10:02:37 | 3686 | |||||||||
|
Trimmomatic Resource Report Resource Website 10000+ mentions |
Trimmomatic (RRID:SCR_011848) | Trimmomatic | software application, data processing software, software resource | Software Java pipeline for trimming tasks for Illumina paired end and single ended data. Flexible Trimmer for Illumina Sequence Data. Pair aware preprocessing tool optimized for Illumina next generation sequencing data. Includes several processing steps for read trimming and filtering. Operating systems Unix/Linux, Mac OS, Windows. | trimming, task, paired, end, single, data, next, generation, sequencing, filtering, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite is related to: shovill |
BLE/BMELV Verbundprojekt ; BMBF |
PMID:24695404 DOI:10.1093/bioinformatics/btu170 |
biotools:trimmomatic, OMICS_01097 | https://omictools.com/trimmomatic-tool https://bio.tools/trimmomatic https://sources.debian.org/src/trimmomatic/ |
SCR_011848 | Trimmomatic v 0.32 | 2026-02-17 10:01:57 | 21028 | |||||
|
ProteinLynx Global Server Resource Report Resource Website 100+ mentions |
ProteinLynx Global Server (RRID:SCR_016664) | PLGS | data or information resource, portal, service resource, organization portal | Platform for quantitative and qualitative proteomics research for Waters Corporation proteomics systems. | Waters Corporation, quantitative, qualitative, proteomics, research, system | is listed by: SoftCite | SCR_016664 | ProteinLynx Global SERVER™ (PLGS), ProteinLynx Global Server, PLGS, ProteinLynx Global Server (PLGS), Protein Lynx Global Server 2.4, Protein Lynx Global Server | 2026-02-17 10:03:27 | 197 |
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