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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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StringTie Resource Report Resource Website 1000+ mentions |
StringTie (RRID:SCR_016323) | data analysis software, data processing software, sequence analysis software, software application, software resource | Software application for assembling of RNA-Seq alignments into potential transcripts. It enables improved reconstruction of a transcriptome from RNA-seq reads. This transcript assembling and quantification program is implemented in C++ . | assembling, RNA, sequence, transcript, gene, alignment, reconstruction, read, analysis, process, bio.tools |
is listed by: bio.tools is listed by: Debian is listed by: OMICtools |
NCI R01 CA120185; NCI R01 CA134292; NHGRI R01 HG006102; NHGRI R01 HG006677; NIGMS R01 GM105705; the Cancer Prevention and Research Institute of Texas |
PMID:25690850 DOI:10.1038/nbt.3122 |
Open source, Free, Freely available, Available for download | biotools:stringtie, OMICS_07226 | https://github.com/gpertea/stringtie, https://bio.tools/stringtie, https://sources.debian.org/src/stringtie/ | SCR_016323 | 2026-09-12 01:00:18 | 4976 | ||||||
|
SVEngine Resource Report Resource Website 1+ mentions |
SVEngine (RRID:SCR_016235) | data analysis software, data processing software, sequence analysis software, simulation software, software application, software resource | Software for analysis and simulation of gene sequences and structural variants. This software works with FASTA, FASTQ, BAM, VAR, META, and NEWICK file formats. | structural, alteration, clonality, NGS, simulator, gene, allele, haplotype, variant | CNSF 61370131; NHGRI R01 HG006137 |
Free, Available to download | SCR_016235 | SVEngine: Allele Specific and Haplotype Aware Structural Variants Simulator | 2026-09-12 01:00:18 | 3 | |||||||||
|
DETONATE Resource Report Resource Website 1+ mentions |
DETONATE (RRID:SCR_017035) | DETONATE | data analysis software, data processing software, sequence analysis software, software application, software resource | Software tool to evaluate de novo transcriptome assemblies from RNA-Seq data. Consists of RSEM-EVAL and REF-EVAL packages. RSEM-EVAL is reference-free evaluation method. REF-EVAL is reference based and can be used to compare sets of any kinds of genomic sequences. | evaluate, de novo, transcriptome, assembly, RNAseq, data, RSEM-EVAL, REF-EVAL, dataset, genomic, sequence, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Wisconsin-Madison; Wisconsin; USA |
NHGRI R01 HG005232; NLM T15 LM007359 |
PMID:25608678 | Free, Available for download, Freely available | biotools:detonate | https://bio.tools/detonate | SCR_017035 | DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation, DETONATE | 2026-09-12 01:00:19 | 2 | ||||
|
miQC Resource Report Resource Website 1+ mentions |
miQC (RRID:SCR_022697) | data analysis software, data processing software, software application, software resource | Software tool as flexible, probablistic metrics for quality control of scRNA-seq data. Adaptive probabilistic framework for quality control of single-cell RNA-sequencing data. Data driven QC metric that jointly models proportion of reads mapping to mtDNA and number of detected genes with mixture models in probabilistic framework to predict which cells are low quality in given dataset. | scRNA-seq data quality control, QC metric, low quality data prediction, single cell RNA-sequencing data | Academy of Finland ; Cancer Foundation Finland ; European Union Horizon 2020 research and innovation program ; NCI CA237170; NHGRI HG009007 |
PMID:34428202 | Free, Available for download, Freely available | SCR_022697 | 2026-09-12 01:00:28 | 4 | |||||||||
|
Reactome Knowledgebase Resource Report Resource Website 500+ mentions |
Reactome Knowledgebase (RRID:SCR_023504) | data access protocol, data or information resource, database, software resource, web service | Open source relational database of signaling and metabolic molecules and their relations organized into biological pathways and processes. Core unit of Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes, vaccines, anti-cancer therapeutics and small molecules) participating in reactions form network of biological interactions and are grouped into pathways including classical intermediary metabolism, signaling, transcriptional regulation, apoptosis and disease. External domain expert provides expertise, curator formalizes it into database structure, and external domain expert reviews representation. System of evidence tracking ensures that all assertions are backed up by primary literature. Website is designed to give the user graphical map of known biological processes and pathways that is also an interface. Database and website enable to find, organize, and utilize biological information to support data visualization, integration and analysis. | signaling and metabolic molecules relations, biological pathways and processes, intermediary metabolism, signaling, transcriptional regulation, apoptosis, disease | NHGRI U24 HG012198 | Free, Freely available | SCR_023504 | Reactome | 2026-09-12 01:00:39 | 872 | |||||||||
|
Michigan Imputation Server Resource Report Resource Website 1+ mentions |
Michigan Imputation Server (RRID:SCR_023554) | data access protocol, software resource, web service | Web based service for imputation that facilitates access to new reference panels and improves user experience and productivity. Server implements whole genotype imputation workflow using MapReduce programming model for efficient parallelization of computationally intensive tasks. Genotype imputation service using Minimac4. | Genotype imputation, whole genotype imputation workflow, parallelization of computationally intensive tasks, | is related to: MINIMAC | Austrian Science Fund ; European Community Seventh Framework Programme ; NHGRI HG000376; NHGRI HG007022; NHLBI HL117626; NIA ; NIDA R01DA037904 |
PMID:27571263 | Free, Freely available | https://github.com/genepi/imputationserver | SCR_023554 | 2026-09-12 01:00:40 | 9 | |||||||
|
Hetnet Connectivity Search Resource Report Resource Website 1+ mentions |
Hetnet Connectivity Search (RRID:SCR_023630) | Hetnet | data access protocol, software resource, web service | Web app that allows users to search for the most important paths connecting any two nodes in Hetionet. | Hetionet, paths connection, paths search, paths connecting any two nodes in Hetionet, | Gordon and Betty Moore Foundation ; NCI R01 CA237170; NHGRI R01 HG010067; NHGRI T32 HG000046; Pfizer Inc |
PMID:36711546 | Free, Freely available | SCR_023630 | , Heterogeneous network Connectivity Search, heterogeneous network | 2026-09-12 01:00:41 | 2 | |||||||
|
ProtParam Tool Resource Report Resource Website 5000+ mentions |
ProtParam Tool (RRID:SCR_018087) | analysis service resource, data analysis software, data processing software, production service resource, sequence analysis software, service resource, software application, software resource | Software tool to calculate various physicochemical parameters for given protein stored in Swiss-Prot or TrEMBL or for user entered protein sequence. Protein can either be pecified as Swiss-Prot/TrEMBL accession number or ID, or in form of raw sequence. Computed parameters include molecular weight, theoretical pI, amino acid composition, atomic composition, extinction coefficient, estimated half-life, instability index, aliphatic index and grand average of hydropathicity. | Calculate phycicochemical parameter, protein, Swiss-Prot, TrEMBL, protein sequence, molecular weight, theortical pl, amino acid composition, atomic composition, extinction coefficient, bio.tools |
is listed by: Debian is listed by: bio.tools is related to: ExPASy Bioinformatics Resource Portal |
NHGRI U01 HG02712; Swiss Federal Government through Federal Office of Education and Science |
PMID:10027275 | Free, Freely available | biotools:protparam | https://bio.tools/protparam | SCR_018087 | ProtParam | 2026-09-12 12:58:57 | 7206 | |||||
|
Combined Annotation Dependent Depletion Resource Report Resource Website 500+ mentions |
Combined Annotation Dependent Depletion (RRID:SCR_018393) | CADD | data access protocol, data analysis software, data processing software, sequence analysis software, service resource, software application, software resource, web service | Web tool for predicting deleteriousness of variants throughout human genome. Software tool for scoring deleteriousness of single nucleotide variants as well as insertion and deletions variants in human genome. | Human genome, disease, prediction, injurious variant, single nucleotide variant, insertion variant, deletion variant, deleteriousness scoring | has parent organization: University of Washington; Seattle; USA | Berlin Institute of Health ; Brotman Baty Institute for Precision Medicine ; Charite University Medicine Berlin ; German Research Foundation ; Howard Hughes Medical Institute ; NCI R01 CA197139; NHGRI U54 HG006493 |
PMID:30371827 PMID:24487276 |
Restricted | SCR_018393 | Combined Annotation Dependent Depletion | 2026-09-12 12:59:00 | 784 | ||||||
|
LRPath Resource Report Resource Website 1+ mentions |
LRPath (RRID:SCR_018572) | analysis service resource, data access protocol, production service resource, service resource, software resource, web service | Web tool to perform gene set enrichment testing. Used to test for predefined biologically relevant gene sets that contain more significant genes from experimental dataset than expected by chance. Logistic regression approach for identifying enriched biological groups in gene expression data. | Gene, map, gene set, gene set testing, identifying enriched biologically group, gene expression data, gene expression, data, bio.tools |
is listed by: bio.tools is listed by: Debian |
NHGRI R01 HG003749; NIDA U54 DA021519; NIEHS P30 ES06096; NIEHS U01 ES015675; NLM R01 LM008106 |
PMID:19038984 | Free, Freely available | biotools:lrpath | https://bio.tools/lrpath | SCR_018572 | 2026-09-12 12:59:02 | 4 | ||||||
|
BRAKER Resource Report Resource Website 500+ mentions |
BRAKER (RRID:SCR_018964) | simulation software, software application, software resource | Software tool as pipeline for accurate and automated gene prediction in novel eukaryotic genomes. Automated gene prediction training and gene prediction pipeline.BRAKER1 is eukaryotic genome annotation pipeline. BRAKER2 is extension of BRAKER1 which allows for fully automated training of gene prediction tools GeneMark EX R14, R15, R17, F1 and AUGUSTUS from RNA Seq and/or protein homology information, and that integrates extrinsic evidence from RNA-Seq and protein homology information into prediction. | Automated gene prediction, novel eukaryotic genomes, gene prediction training, gene prediction pipeline, protein coding gene structure, gene structure prediction, eukaryotic genome, RNA-Seq, protein homology |
uses: Augustus is listed by: Debian is listed by: OMICtools |
German Research Foundation ; NHGRI HG000783 |
PMID:31020555 DOI:10.1101/2020.08.10.245134 |
Free, Available for download, Freely available | OMICS_10582 | https://sources.debian.org/src/braker/ | SCR_018964 | BRAKER2, BRAKER1 | 2026-09-12 12:59:08 | 531 | |||||
|
LocusZoom.org Resource Report Resource Website 10+ mentions |
LocusZoom.org (RRID:SCR_021374) | data access protocol, software resource, web service | Web tool to investigate genome wide association results in their local genomic context. Adds new features to LocusZoom such as Manhattan plots, annotation options, and calculations that put findings in context. Used for interactive and embeddable visualization of genetic association study results.Javascript/d3 embeddable plugin for interactively visualizing statistical genetic data from customizable sources. | Generate interactive plots, shareable plots, GWAS summary statistics, visualizing statistical genetic data, genetic association study | NHGRI HG009976; NIH BOEH15AMP |
DOI:10.1093/bioinformatics/btab186 | Free, Freely available | SCR_021374 | LocusZoom.js | 2026-09-12 12:59:54 | 41 | ||||||||
|
CRISPResso Resource Report Resource Website 10+ mentions |
CRISPResso (RRID:SCR_021538) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | Software suite of tools to qualitatively and quantitatively evaluate outcomes of genome editing experiments in which target loci are subject to deep sequencing and provides integrated, user friendly interface. Used for analysis of CRISPR-Cas9 genome editing outcomes from sequencing data. CRISPResso2 provides accurate and rapid genome editing sequence analysis.Used for analysis of deep sequencing data for rapid and intuitive interpretation of genome editing experiments. | Quantification, visualization, CRISPR-Cas9 outcomes, coding sequences evaluation, noncoding elements evaluation, selected off target sites evaluation, genome editing evaluation. | NHGRI R00 HG008399; NHGRI R01 HG005085; NHGRI RM1 HG009490; NHLBI P01 HL32262; NHLBI R01 HL119099; NIBIB R01 EB022376; NIDDK P30 DK049216; NIDDK R03 DK109232; NIGMS R35 GM118062; NIGMS R35 GM118158 |
PMID:27404874 PMID:30809026 |
Free, Available for download, Freely available | https://github.com/pinellolab/CRISPResso2, https://github.com/pinellolab/CRISPResso | SCR_021538 | CRISPResso2 | 2026-09-12 12:59:57 | 27 | |||||||
|
SALSA Resource Report Resource Website 10+ mentions |
SALSA (RRID:SCR_022013) | data analysis software, data processing software, software application, software resource | Software tool for scaffold long read assemblies with Hi-C data. | scaffolding, Hi-C data, scaffold long read assemblies | Ministry of Health and Welfare ; Republic of Korea ; NHGRI R44 HG009584; NIAID R01 AI100947 |
DOI:10.1371/journal.pcbi.1007273 DOI:10.1186/s12864-017-3879-z |
Free, Available for download, Freely available | SCR_022013 | SALSA2 | 2026-09-12 01:00:04 | 46 | ||||||||
|
CHOPCHOP Resource Report Resource Website 1000+ mentions |
CHOPCHOP (RRID:SCR_015723) | authoring tool, software application, software resource, web application | Web application for designing gRNAs for CRISPR/Cas9 experiments. It selects target sites for CRISPR/Cas9, CRISPR/Cpf1 or TALEN-directed mutagenesis. | mutagenesis, talen, grna, crispr, cas9, cpf1, experiment design, target site, genetic engineering | NHGRI P50 HG005550 | PMID:24861617 PMID:27185894 |
Freely available | SCR_015723 | CHOPCHOP v2 | 2026-09-12 12:58:29 | 2045 | ||||||||
|
Poretools Resource Report Resource Website 50+ mentions |
Poretools (RRID:SCR_015879) | data analysis software, data processing software, sequence analysis software, software application, software resource, software toolkit | 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 | 2026-09-12 12:58:32 | 83 | ||||||
|
Bamtools Resource Report Resource Website 100+ mentions |
Bamtools (RRID:SCR_015987) | data analysis software, data management software, data processing software, software application, software resource, software toolkit | 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 | 2026-09-12 12:58:33 | 344 | ||||||
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Blixem Resource Report Resource Website 1+ mentions |
Blixem (RRID:SCR_015994) | alignment software, data processing software, image analysis software, software application, software resource | Software for sequence alignments that displays multiple match sequences aligned against a single genomic reference sequence. It can be used for manipulation, display and annotation of genomic data, to check the quality of an alignment, to find missing/misaligned sequence, and to identify splice sites and polyA sites. | software, sequence, alignment, annotation, genomic, reference, data, display, manipulation, DNA |
is related to: SEQtools has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom |
NHGRI U54 HG00455; Wellcome Trust Grant 098051 |
PMID:26801397 | Free, Available for download | SCR_015994 | SEQtools Blixem | 2026-09-12 12:58:34 | 2 | |||||||
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AMAP Resource Report Resource Website 100+ mentions |
AMAP (RRID:SCR_015969) | alignment software, data processing software, image analysis software, software application, software resource, source code | Source code that performs multiple alignment of peptidic sequences. It utilizes posterior decoding and a sequence-annealing alignment, instead of the traditional progressive alignment method. | software, peptide, sequence, alignment, annealing, bioinformatics, multiple, svn, posterior, decoding |
is listed by: Debian is listed by: OMICtools has parent organization: University of California at Berkeley; Berkeley; USA |
NHGRI R01 HG2362; NSF CCF0347992; NSF EF 03-31494 |
PMID:17237099 DOI:10.1093/bioinformatics/btl311 |
Free, Available for download | OMICS_19787 | http://baboon.math.berkeley.edu/amap/, https://sources.debian.org/src/amap-align/ | https://sources.debian.org/src/amos-assembler/ | SCR_015969 | amap-align | 2026-09-12 12:58:33 | 400 | ||||
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GenomeScope Resource Report Resource Website 500+ mentions |
GenomeScope (RRID:SCR_017014) | Genomescope | data analysis software, data processing software, service resource, software application, software resource | Open source software package for fast genome analysis from unassembled short reads. Used to estimate genome heterozygosity, repeat content, and size from sequencing reads using a kmer-based statistical approach. | genome, unassembled, sequenced, data, short, read, analysis, heterozygosity, repeat, content, size, kmer | is related to: Cold Spring Harbor Laboratory | NHGRI R01 HG006677; NSF DBI 1350041; NSF IOS 1237880 |
PMID:28369201 | Free, Freely available, | http://qb.cshl.edu/genomescope/ | SCR_017014 | 2026-09-12 12:58:47 | 800 |
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