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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Drop-seq tools Resource Report Resource Website 50+ mentions |
Drop-seq tools (RRID:SCR_018142) | data analysis software, software resource, data processing software, software application | Software Java tools for analyzing Drop-seq data. Used to analyze gene expression from thousands of individual cells simultaneously. Analyzes mRNA transcripts while remembering origin cell transcript. | Simultaneous analysis, Drop-seq data, gene expression, thousands individual cells |
is listed by: Debian has parent organization: Broad Institute |
Stanley Center for Psychiatric Research ; MGH Psychiatry Residency Research Program ; Stanley-MGH Fellowship in Psychiatric Neuroscience ; Stewart Trust Fellows Award ; Simons Foundation ; NHGRI P50 HG006193; Klarman Cell Observatory ; NIMH U01 MH105960; NIMH R25 MH094612; NICHD F32 HD075541; NSF ECS 0335765; NSF DMR 1310266; NSF DMR 1420570 |
PMID:26000488 | https://sources.debian.org/src/drop-seq-tools/ | SCR_018142 | Droplet sequencing tools, Droplet sequencing data analysis software tools | 2026-02-13 10:58:07 | 94 | |||||||
|
Shannon Resource Report Resource Website 1+ mentions |
Shannon (RRID:SCR_017037) | data analysis software, software resource, data processing software, software application | Software tool for de novo transcriptome assembly from RNA-Seq data. | de novo, transcriptome, assembly, RNAseq, data |
has parent organization: University of Washington; Seattle; USA has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Stanford University; Stanford; California |
NSF Center for Science of Information ; NHGRI ; University of Washington |
Free, Available for download, Freely available | http://sreeramkannan.github.io/Shannon/ | SCR_017037 | 2026-02-13 10:57:55 | 1 | ||||||||
|
SNPRelate Resource Report Resource Website 10+ mentions |
SNPRelate (RRID:SCR_022719) | data analysis software, software resource, data processing software, software application | Software R package as parallel computing toolset for relatedness and principal component analysis of SNP data. | parallel computing, relatedness and principal component analysis, SNP data analysis | NHGRI U01 HG 004446 | PMID:23060615 | Free, Available for download, Freely available | https://github.com/zhengxwen/SNPRelate | SCR_022719 | 2026-02-13 10:58:47 | 12 | ||||||||
|
hifiasm-meta Resource Report Resource Website 1+ mentions |
hifiasm-meta (RRID:SCR_022771) | data analysis software, software resource, data processing software, software application | Software tool as metagenome assembler that exploits high accuracy of recent data. De novo metagenome assembler, based on haplotype resolved de novo assembler for PacBio Hifi reads. Workflow consists of optional read selection, sequencing error correction, read overlapping, string graph construction and graph cleaning. | Error correction, read overlapping, hifiasm, haplotype resolved de novo assembler, PacBio Hifi reads | NHGRI R01HG010040; NHGRI U01HG010971 |
PMID:35534630 | Free, Available for download, Freely available | SCR_022771 | hifiasm_meta | 2026-02-13 10:58:53 | 2 | ||||||||
|
ComplexUpset Resource Report Resource Website 10+ mentions |
ComplexUpset (RRID:SCR_022752) | data analysis software, software resource, data processing software, software application | Software R package for visualization of intersecting sets. Used for quantitative analysis of sets, their intersections, and aggregates of intersections. Visualizes set intersections in matrix layout and introduces aggregates based on groupings and queries. | visualization of intersecting sets, set intSections in matrix layout, aggregates based on groupings and queries, quantitative analysis of sets |
uses: ggplot2 is listed by: CRAN |
Austrian Science Fund ; Air Force Research Laboratory and DARPA ; NHGRI K99 HG007583 |
PMID:26356912 | Free, Available for download, Freely available | SCR_022752 | 2026-02-13 10:58:47 | 18 | ||||||||
|
sei Resource Report Resource Website 1+ mentions |
sei (RRID:SCR_022571) | data access protocol, software resource, web service | Web server for systematically predicting sequence regulatory activities and applying sequence information to human genetics data. Provides global map from any sequence to regulatory activities, as represented by sequence classes, and each sequence class integrates predictions for chromatin profiles like transcription factor, histone marks, and chromatin accessibility profiles across wide range of cell types. | systematically predicting sequence regulatory activities, applying sequence information, human genetics data, sequence class predictions | National Science Foundation Graduate Research Fellowship Program ; NHGRI R01HG005998; NHLBI U54HL117798; NIGMS R01GM071966 |
PMID:35817977 | Free, Available for download, Freely available | https://hb.flatironinstitute.org/sei | SCR_022571 | 2026-02-13 10:58:52 | 6 | ||||||||
|
UpSet Resource Report Resource Website 10+ mentions |
UpSet (RRID:SCR_022731) | data visualization software, data processing software, data analysis software, software application, software resource | Software tool to visualize set intersections in matrix layout. Interactive, web based visualization technique designed to analyze set based data. Visualizes both, set intersections and their properties, and elements in dataset. Used for quantitative analysis of data with more than three sets. | visualize set intersections, matrix layout, intersecting sets, more than three sets quantitative data analysis | Austrian Science Fund ; Air Force Research Laboratory ; DARPA ; NHGRI K99 HG007583 |
PMID:26356912 | Free, Available for download, Freely available | https://github.com/VCG/upset | SCR_022731 | UpSet Plot | 2026-02-13 10:58:47 | 16 | |||||||
|
SvABA Resource Report Resource Website 10+ mentions |
SvABA (RRID:SCR_022998) | sequence analysis software, data processing software, data analysis software, software application, software resource | Software tool for detecting structural variants in sequencing data using genome wide local assembly. Genome wide detection of structural variants and indels by local assembly. Used for detecting SVs from short read sequencing data using genome wide local assembly with low memory and computing requirements. | genome wide detection, structural variants, indels, local assembly | NHGRI T32 HG002295; NCI U54CA143798; NCI R01CA188228; DFCI-Novartis Drug Discovery Program ; Voices Against Brain Cancer ; Pediatric Low-Grade Astrocytoma Foundation ; Broad Institute ; Wellcome Fund Career Award for Medical Scientists |
PMID:29535149 | Free, Available for download, Freely available | SCR_022998 | 2026-02-13 10:58:58 | 14 | |||||||||
|
WTDBG Resource Report Resource Website 50+ mentions |
WTDBG (RRID:SCR_017225) | sequence analysis software, data processing software, alignment software, data analysis software, software application, software resource, image analysis software | Software tool as de novo sequence assembler for long noisy reads produced by PacBio or Oxford Nanopore Technologies. It assembles raw reads without error correction and then builds consensus from intermediate assembly output. Desiged to assemble huge genomes in very limited time. | sequence, assembler, de novo, long, noisy, read, likelihood, estimator, genome |
is listed by: OMICtools is listed by: Debian |
NSFC ; NHGRI R01 HG010040 |
PMID:31819265 | Free, Available for download, Freely available | OMICS_24025 | https://github.com/ruanjue/wtdbg https://sources.debian.org/src/wtdbg2/ |
SCR_017225 | Wtdbg2, wtdgb, Wtdgb, wtdgb2 | 2026-02-13 10:57:53 | 57 | |||||
|
Ngmlr Resource Report Resource Website 10+ mentions |
Ngmlr (RRID:SCR_017620) | NGMLR | data processing software, alignment software, software application, software resource, image analysis software | Software tool as long read mapper designed to align PacBio or Oxford Nanopore reads to reference genome and optimized for structural variation detection. | Long, read, mapper, align, PacBio, Oxford Nanopore, read, reference, genome, structural, variantion, detection, bio.tools |
is listed by: bio.tools is listed by: Debian |
National Science Foundation ; NHGRI R01 HG006677; NHGRI UM1 HG008898 |
PMID:29713083 | Free, Available for download, Freely available | biotools:ngmlr | https://bio.tools/ngmlr | SCR_017620 | coNvex Gap-cost alignMent for Long Reads | 2026-02-13 10:58:06 | 31 | ||||
|
ChromHMM Resource Report Resource Website 10+ mentions |
ChromHMM (RRID:SCR_018141) | data analysis software, software resource, data processing software, software application | Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations. | Chromatin state discovery, chromatin characterization, genome annotation, non coding genome, epigenomic, cell, annotation, analysis, pattern |
is listed by: Debian is listed by: OMICtools |
NHGRI U54 HG004570; NHGRI RC1HG005334; NIEHS R01 ES024995; NHGRI U01 HG007912; NIMH U01 MH105578; NSF 0905968; Alfred P. Sloan Fellowship ; CAREER Award |
PMID:29120462 PMID:22373907 |
Free, Available for download, Freely available | OMICS_03490 | https://sources.debian.org/src/chromhmm/ | SCR_018141 | 2026-02-13 10:58:09 | 47 | ||||||
|
NanoSim Resource Report Resource Website 10+ mentions |
NanoSim (RRID:SCR_018243) | software resource, simulation software, software application | Software tool as Nanopore sequence read simulator based on statistical characterization. Oxford Nanopore Technology sequence simulator written in Python and R. Benefits development of scalable next generation sequencing technologies for long nanopore reads, including genome assembly, mutation detection, and metagenomic analysis software. | Nanopore sequence read, sequence simulator, Oxford Nanopore Technology, next generation sequencing, long nanopore read, genome assembly, mutation detection, bio.tools, bio.tools |
is listed by: Debian is listed by: bio.tools |
NHGRI R01 HG007182; Genome Canada ; Genome British Columbia ; British Columbia Cancer Foundation ; University of British Columbia |
DOI:10.1093/gigascience/gix010 | Free, Available for download, Freely available | biotools:trans-nanosim, biotools:nanosim | https://www.bcgsc.ca/resources/software/nanosim https://bio.tools/nanosim https://bio.tools/Trans-NanoSim |
SCR_018243 | 2026-02-13 10:58:19 | 18 | ||||||
|
Minimap2 Resource Report Resource Website 1000+ mentions |
Minimap2 (RRID:SCR_018550) | data processing software, alignment software, software application, software resource, image analysis software | Software tool as pairwise alignment for nucleotide sequences. Alignment program to map DNA or long mRNA sequences against large reference database. Versatile pairwise aligner for genomic and spliced nucleotide sequences. | Pairwise alignment, nucleotide sequence, map DNA sequence, map mRNA sequence, reference database, spliced nucleotide sequence, bio.tools, FASEB list |
is used by: D-GENIES is listed by: Debian is listed by: bio.tools is listed by: OMICtools |
NHGRI R01 HG010040 | PMID:29750242 | Free, Available for download, Freely available | OMICS_31658, biotools:minimap2 | https://bio.tools/minimap2 https://sources.debian.org/src/libminimap2-dev/ |
SCR_018550 | 2026-02-13 10:58:13 | 1325 | ||||||
|
Monocle3 Resource Report Resource Website 100+ mentions |
Monocle3 (RRID:SCR_018685) | data processing software, data analysis software, software toolkit, software application, software resource | Software analysis toolkit for single cell RNA-seq. Used for single cell RNA-Seq experiments. Unsupervised algorithm that increases temporal resolution of transcriptome dynamics using single-cell RNA-Seq data collected at multiple time points. | Data analysis, singel cell RNAseq data, single cell RNAseq experiment, transcriptome dynamics | has parent organization: University of Washington; Seattle; USA | NIH Office of the Director DP2 OD00667; NIGMS P01 GM099117; NIH Office of the Director DP2 0D008514; NHGRI P50 HG006193; Single Cell Genomics initiative |
PMID:24658644 | Free, Available for download, Freely available | https://github.com/cole-trapnell-lab/monocle3 | SCR_018685 | Monocle, Monocle 3 | 2026-02-13 10:58:16 | 270 | ||||||
|
QoRTs Resource Report Resource Website 10+ mentions |
QoRTs (RRID:SCR_018665) | data processing software, data analysis software, software toolkit, software application, software resource | Software package for quality control and data processing of RNA-Seq experiments. Software portable multifunction toolkit for assisting in analysis, quality control, and data management of RNA-Seq and DNA-Seq datasets. Used for detection and identification of errors, biases, and artifacts produced by high throughput sequencing technology. Can be used in operating system that supports Java and R. | Quality control, data processing, RNAseq data, DNAseq data, analysis, data management, error detection, biases, artifacts, high throughput sequencing technology, | NHGRI | PMID:26187896 | Free, Freely available | https://github.com/hartleys/QoRTs | SCR_018665 | 2026-02-13 10:58:15 | 26 | ||||||||
|
MyGene.info Resource Report Resource Website 10+ mentions |
MyGene.info (RRID:SCR_018660) | data access protocol, software resource, web service, service resource | Web service for querying or retrieving gene annotation data. | Querying gene, gene, annotation, gene annotation, annotation data, gene annotation data, retrieving gene annotation data, bio.tools |
is listed by: Debian is listed by: bio.tools |
NHGRI U01 HG008473; NIGMS GM083924; NIGMS U54 GM114833; NHGRI U01 HG006476; NCI K22 CA188163; NCATS UL1 TR001114; Scripps Translational Science Institute |
DOI:10.1186/s13059-016-0953-9 | Free, Freely available | biotools:mygene.info, BioTools:mygene.info | https://bio.tools/mygene.info https://bio.tools/mygene.info https://bio.tools/mygene.info |
SCR_018660 | 2026-02-13 10:58:16 | 20 | ||||||
|
riborex Resource Report Resource Website 1+ mentions |
riborex (RRID:SCR_019104) | software resource, software toolkit | Software R package for identification of differential translation from Ribo-seq data. Computational tool for mapping genome wide differences in translation efficiency. | Ribo-seq data, differential translation, differential translation identification, mapping genome differences, translation efficiency, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: University of Southern California; Los Angeles; USA |
NHGRI R01 HG006015 | PMID:28158331 | Free, Available for download, Freely available | biotools:riborex | https://bio.tools/riborex | SCR_019104 | riborex v2.3.4 | 2026-02-13 10:58:20 | 7 | |||||
|
Epiviz Resource Report Resource Website 1+ mentions |
Epiviz (RRID:SCR_022796) | software resource, software toolkit | Software package as interactive visualization tool for functional genomics data. Interactive visual analytics for functional genomics data. | Interactive visual analytics, functional genomics data, interactive visualization tool | is provided by: BICCN | NHGRI R01 HG006102; NHGRI R01 HG005220; Illumina Corporation ; Genentech |
PMID:25086505 | Free, Available for download, Freely available | https://bioconductor.org/packages/epivizr/ https://epiviz.github.io/ |
SCR_022796 | 2026-02-13 10:58:54 | 1 | |||||||
|
ataqv Resource Report Resource Website 1+ mentions |
ataqv (RRID:SCR_023112) | software resource, software toolkit | Software package for QC and visualization of ATAC-seq results. Used to examine aligned reads and report basic metrics, including reads mapped in proper pairs, optical or PCR duplicates, reads mapping to autosomal or mitochondrial references, ratio of short to mononucleosomal fragment counts, mapping quality, various kinds of problematic alignments. | QC of ATAC-seq results, visualization of ATAC-seq results, examine aligned reads, mapping quality, | NIDDK R01 DK-117960; American Diabetes Association Pathway to Stop Diabetes ; NHGRI T32 HG00040; NIDDK T32 DK101357; University of Michigan Rackham Predoctoral Fellowship |
PMID:32213349 | Free, Available for download, Freely available | https://parkerlab.github.io/ataqv/demo/ | SCR_023112 | 2026-02-13 10:58:56 | 6 | ||||||||
|
SURVIVOR Resource Report Resource Website 10+ mentions |
SURVIVOR (RRID:SCR_022995) | SURVIVOR | software resource, software toolkit | Software tool set for simulating and evaluating SVs, merging and comparing SVs within and among samples, and includes various methods to reformat or summarize SVs. Used for for SV simulation, comparison and filtering. | Structural Variant, simulating and evaluating SVs, merging and comparing SVs, reformat or summarize SVs, | Swiss National Science Foundation ; National Science Foundation DBI-1350041; NHGRI R01-HG006677; Wellcome Trust Senior Investigator Award ; Royal Society Wolfson Research Merit Award ; EPSRC Centre for Doctoral Training studentship at UCL CoMPLEX |
PMID:28117401 | Free, Available for download, Freely available | SCR_022995 | StructURal Variant majorIty VOte | 2026-02-13 10:58:50 | 15 |
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