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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
RevMan Resource Report Resource Website 10000+ mentions |
RevMan (RRID:SCR_003581) | RevMan | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 5, 2023.A software package that does meta-analysis and provides results in tabular format and graphically., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools is listed by: SoftCite |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00244 | SCR_003581 | Review Manager | 2026-02-07 02:06:23 | 12959 | ||||||||
|
PyroBayes Resource Report Resource Website 1+ mentions |
PyroBayes (RRID:SCR_003757) | PyroBayes | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. A base caller for pyrosequences from the 454 Life Sciences sequencing machines. | is listed by: OMICtools | PMID:18193056 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01155 | SCR_003757 | 2026-02-07 02:06:26 | 3 | ||||||||
|
RAREMETAL Resource Report Resource Website 10+ mentions |
RAREMETAL (RRID:SCR_003573) | RAREMETAL | software resource | A software program that facilitates the meta-analysis of rare variants from genotype arrays or sequencing. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Michigan; Ann Arbor; USA |
PMID:24894501 | biotools:raremetal, OMICS_00243 | https://bio.tools/raremetal | SCR_003573 | 2026-02-07 02:06:05 | 22 | |||||||
|
PEAR Resource Report Resource Website 500+ mentions |
PEAR (RRID:SCR_003776) | PEAR | software resource | Software for an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory. | next-generation sequencing, sequence analysis |
is listed by: OMICtools has parent organization: Heidelberg Institute for Theoretical Studies; Heidelberg; Germany |
PMID:24142950 | OMICS_00674 | SCR_003776 | Pair-end read merger, PEAR: Pair-end read merger | 2026-02-07 02:06:26 | 839 | |||||||
|
SeqExpress Resource Report Resource Website |
SeqExpress (RRID:SCR_004013) | software resource | A cross-platform software that estimates gene/isoform expression level via mRNA-Seq data. SeqExpress exams the Sequencing bias in mRNA-Seq and correct it to get more accurate estimation. | c++, mrna-seq, qt |
is listed by: OMICtools has parent organization: SourceForge |
PMID:15746290 PMID:14988116 |
GNU General Public License v2 | OMICS_01289 | SCR_004013 | 2026-02-07 02:06:13 | 0 | ||||||||
|
MSG Resource Report Resource Website 1+ mentions |
MSG (RRID:SCR_004161) | MSG | software resource | A pipeline of scripts to assign ancestry to genomic segments using next-gen sequence data. This method can identify recombination breakpoints in a large number of individuals simultaneously at a resolution sufficient for most mapping purposes, such as quantitative trait locus (QTL) mapping and mapping of induced mutations. | next generation sequencing, genotyping, genetic mapping, ancestry, genome |
is listed by: OMICtools has parent organization: Princeton University; New Jersey; USA |
PMID:21233398 | OMICS_01551 | SCR_004161 | Multiplexed shotgun genotyping, Multiplexed shotgun genotyping (MSG), MSG: Multiplexed Shotgun Genotyping | 2026-02-07 02:06:19 | 2 | |||||||
|
PerM Resource Report Resource Website 50+ mentions |
PerM (RRID:SCR_004223) | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software package to perform highly efficient genome scale alignments for hundreds of millions of short reads produced by the ABI SOLiD and Illumina sequencing platforms. It capable of providing full sensitivity for alignments within 4 mismatches for 50bp SOLID reads and 9 mismatches for 100bp Illumina reads.Efficient mapping of short sequencing reads with periodic full sensitive spaced seeds. | Short sequencing mapping, short sequencing read, next-generation sequencing, genome, alignment, short read, abi, solid, illumina, , bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Clippers has parent organization: Google Code has parent organization: University of Southern California; Los Angeles; USA |
PMID:19675096 DOI:10.1093/bioinformatics/btp486 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00675, biotools:perm | https://bio.tools/perm https://sources.debian.org/src/perm/ |
SCR_004223 | PERiodic seed Mapping, Periodic seed Mapping | 2026-02-07 02:06:20 | 60 | ||||||
|
HLASeq Resource Report Resource Website |
HLASeq (RRID:SCR_004185) | HLASeq | software resource | An open-source software tool for accurate genotyping the human HLA genes from Illumina GA high-throughput sequencing data. | genotyping, hla, next generation sequencing, gene, command-line, python |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v3 | OMICS_01543 | SCR_004185 | 2026-02-07 02:06:40 | 0 | ||||||||
|
PASS-bis Resource Report Resource Website |
PASS-bis (RRID:SCR_004176) | PASS-bis | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 9, 2023. A bisulfite aligner suitable for whole methylome analysis of Illumina and SOLiD reads. |
is listed by: OMICtools is related to: PASS |
PMID:23162053 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00587 | SCR_004176 | 2026-02-07 02:06:40 | 0 | ||||||||
|
DRUT Resource Report Resource Website |
DRUT (RRID:SCR_004351) | DRUT | software resource | Software for Discovery and Reconstruction of Unannotated Transcripts in Partially Annotated Genomes from High-Throughput RNA-Seq Data. | c++, reconstruction, frequency estimation, transcript, rna-seq, annotation |
is listed by: OMICtools has parent organization: Georgia State University; Georgia; USA |
NSF IIS-0546457; NSF IIS-0916401; NSF IIS-0916948 |
PMID:23202426 | OMICS_01273 | SCR_004351 | Discovery and Reconstruction of Unannotated Transcripts | 2026-02-07 02:06:22 | 0 | ||||||
|
PALMapper Resource Report Resource Website 1+ mentions |
PALMapper (RRID:SCR_011466) | PALMapper | software resource | Computes both spliced and unspliced alignments at high accuracy while taking advantage of base quality information and splice site predictions. | is listed by: OMICtools | OMICS_01245 | SCR_011466 | 2026-02-07 02:08:18 | 4 | ||||||||||
|
PiMS Resource Report Resource Website 100+ mentions |
PiMS (RRID:SCR_011816) | PiMS | software resource | Software for a Laboratory Information Management System (LIMS) developed to support the unpredictable workflows of Molecular biology and Protein production labs of all sizes. | protein | is listed by: OMICtools | BBSRC ; CCP4 ; Instruct |
PMID:21385349 | Free for academic use | OMICS_01010 | SCR_011816 | Protein Information Management System | 2026-02-07 02:08:22 | 187 | |||||
|
Galaxy LIMS Resource Report Resource Website |
Galaxy LIMS (RRID:SCR_011829) | Galaxy LIMS | software resource | A laboratory information management system (LIMS) for a next-generation sequencing (NGS) laboratory within the existing Galaxy platform. | is listed by: OMICtools | BMBF | PMID:23479349 | OMICS_01004 | SCR_011829 | 2026-02-07 02:08:24 | 0 | ||||||||
|
GPU-BLAST Resource Report Resource Website |
GPU-BLAST (RRID:SCR_011820) | GPU-BLAST | software resource | Software for an accelerated version of the popular NCBI-BLAST using a general-purpose graphics processing unit (GPU). It s nearly four times faster, while producing identical results. GPU-BLAST supports: protein alignment according to blastp (it does not support psiblast), multiple CPU threads working in parallel with a single GPU, and input files with multiple protein queries. | c++, gpu/cuda |
is listed by: OMICtools has parent organization: Carnegie Mellon University; Pennsylvania; USA |
PMID:21088027 | Free, Public, Acknowledgement requested | OMICS_00995 | http://eudoxus.cheme.cmu.edu/gpublast/gpublast.html | SCR_011820 | 2026-02-07 02:08:24 | 0 | ||||||
|
IGB Resource Report Resource Website 100+ mentions |
IGB (RRID:SCR_011792) | IGB | software resource | An easy-to-use, highly customizable genome browser you can use to visualize and explore genomic data and annotations, including RNA-Seq, ChIP-Seq, tiling array data, and more. | genome, rna-seq, chip-seq, tiling array, browser |
is listed by: OMICtools has parent organization: University of North Carolina at Charlotte; North Carolina; USA |
PMID:19654113 | Free, Acknowledgement requested | OMICS_00916 | SCR_011792 | Integrated Genome Browser | 2026-02-07 02:08:23 | 326 | ||||||
|
Integrative Genomics Viewer Resource Report Resource Website 500+ mentions |
Integrative Genomics Viewer (RRID:SCR_011793) | IGV | software resource | A high-performance visualization tool for interactive exploration of large, integrated genomic datasets. | genomic datasets exploration, |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is listed by: SoftCite has parent organization: Broad Institute |
DOI:10.1038/nbt.1754 | OMICS_00917, biotools:igv | https://bio.tools/igv https://sources.debian.org/src/igv/ |
SCR_011793 | 2026-02-07 02:08:21 | 789 | |||||||
|
NCBI Genome Workbench Resource Report Resource Website 10+ mentions |
NCBI Genome Workbench (RRID:SCR_011794) | Genome Workbench | software resource | An integrated application for viewing and analyzing sequence data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: NCBI |
OMICS_00920, biotools:ncbi_genome_workbench | https://bio.tools/ncbi_genome_workbench | SCR_011794 | 2026-02-07 02:08:15 | 11 | ||||||||
|
ngs.plot Resource Report Resource Website 10+ mentions |
ngs.plot (RRID:SCR_011795) | ngs.plot | software resource | A software program that allows you to easily visualize your next-generation sequencing (NGS) samples at functional genomic regions. | bio.tools, FASEB list |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
GNU General Public License, v3 | BioTools:ngs.plot, OMICS_00922, biotools:ngs.plot | https://bio.tools/ngs.plot https://bio.tools/ngs.plot https://bio.tools/ngs.plot |
SCR_011795 | ngsplot, ngsplot - Quick mining and visualization of next-generation sequencing data by integrating genomic databases | 2026-02-07 02:08:24 | 42 | ||||||
|
MizBee Resource Report Resource Website 1+ mentions |
MizBee (RRID:SCR_011804) | MizBee | software resource | A multiscale synteny browser for exploring conservation relationships in comparative genomics data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Utah; Utah; USA |
OMICS_00943, biotools:mizbee | https://bio.tools/mizbee | SCR_011804 | MizBee - A Multiscale Synteny Browser | 2026-02-07 02:08:15 | 2 | |||||||
|
PipMaker and MultiPipMaker Resource Report Resource Website 50+ mentions |
PipMaker and MultiPipMaker (RRID:SCR_011806) | PipMaker and MultiPipMaker | software resource | PipMaker computes alignments of similar regions in two DNA sequences. Moreover, MultiPipMaker can be requested to compute a true multiple alignment of the input sequences and return a nucleotide-level view of the results. |
is listed by: OMICtools has parent organization: Pennsylvania State University |
OMICS_00944 | SCR_011806 | 2026-02-07 02:08:15 | 78 |
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