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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Flexbar Resource Report Resource Website 100+ mentions |
Flexbar (RRID:SCR_013001) | Flexbar | software resource | Flexible barcode and adapter removal for sequencing platforms. | bio.tools |
is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
DOI:10.3390/biology1030895 | biotools:flexbar | https://bio.tools/flexbar, https://sources.debian.org/src/flexbar/ | SCR_013001 | SciCrunch Registry | 2026-10-31 12:15:52 | 307 | |||||||
|
SHREC Resource Report Resource Website 10+ mentions |
SHREC (RRID:SCR_013009) | SHREC | software resource | A bioinformatics tool for error correction of HTS read data. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01110 | SCR_013009 | SciCrunch Registry | 2026-10-31 12:15:56 | 14 | ||||||||||
|
hiCtools Resource Report Resource Website |
hiCtools (RRID:SCR_013010) | hiCtools | software resource | This collection of tools stream-lines the processing of HiC data from raw sequence to contact matrices and beyond. |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v3 | OMICS_00522 | SCR_013010 | SciCrunch Registry | 2026-10-31 12:15:50 | 0 | |||||||||
|
AutoMap Resource Report Resource Website 100+ mentions |
AutoMap (RRID:SCR_013095) | AutoMap | software resource | A tool for structural biology and drug design. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01596 | SCR_013095 | SciCrunch Registry | 2026-10-31 12:15:58 | 100 | ||||||||||
|
LOCAS Resource Report Resource Website 1+ mentions |
LOCAS (RRID:SCR_013064) | LOCAS | software resource | A software to assemble short reads of next generation sequencing technologies at low coverage. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
PMID:21858125 | OMICS_00019, biotools:locas | https://bio.tools/locas | SCR_013064 | SciCrunch Registry | 2026-10-31 12:15:54 | 2 | |||||||
|
VDJFasta Resource Report Resource Website 1+ mentions |
VDJFasta (RRID:SCR_013069) | VDJFasta | software resource | Bioinformatics Perl extension for the analysis of antibody variable domain repertoires. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:19875695 | OMICS_00004 | SCR_013069 | SciCrunch Registry | 2026-10-31 12:15:58 | 9 | |||||||||
|
VCAKE Resource Report Resource Website 1+ mentions |
VCAKE (RRID:SCR_013060) | VCAKE | software resource | A genetic sequence assembler capable of assembling millions of small nucleotide reads even in the presence of sequencing error. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00037 | SCR_013060 | SciCrunch Registry | 2026-10-31 12:15:51 | 4 | ||||||||||
|
CoNIFER Resource Report Resource Website 100+ mentions |
CoNIFER (RRID:SCR_013213) | CoNIFER | software resource | Uses exome sequencing data to find copy number variants (CNVs) and genotype the copy-number of duplicated genes. |
is listed by: OMICtools has parent organization: SourceForge |
Commercial license | OMICS_00330 | SCR_013213 | SciCrunch Registry | Copy Number Inference From Exome Reads | 2026-10-31 12:15:56 | 200 | ||||||||
|
RDXplorer Resource Report Resource Website 1+ mentions |
RDXplorer (RRID:SCR_013290) | RDXplorer | software resource | A computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge |
biotools:RDXplorer, OMICS_00349 | https://bio.tools/RDXplorer | SCR_013290 | SciCrunch Registry | 2026-10-31 12:16:02 | 7 | ||||||||
|
Neuroimaging in Python Resource Report Resource Website 10+ mentions |
Neuroimaging in Python (RRID:SCR_013141) | NIPY, | community building portal, data or information resource, portal, software application, software development environment, software development tool, software resource | Community site to make brain imaging research easier that aims to build software that is clearly written, clearly explained, a good fit for the underlying ideas, and a natural home for collaboration. | brain, imaging, neuroimaging, analysis, python, fmri, fmri analysis, magnetic resonance |
is listed by: NeuroImaging Tools and Resources Collaboratory (NITRC) is related to: Python Programming Language has parent organization: SourceForge has parent organization: University of California at Berkeley; Berkeley; USA has parent organization: Massachusetts Institute of Technology; Massachusetts; USA; is parent organization of: Dipy is parent organization of: NiLearn is parent organization of: NIPY is parent organization of: NiBabel is parent organization of: Nipype is parent organization of: Nitime |
NIMH 5R01MH081909-02; NIBIB 1R03EB008673-01 |
PMID:21897815 | Revised BSD license | nlx_149365 | http://www.nitrc.org/projects/nipy-community http://www.nitrc.org/projects/nipype | SCR_013141 | SciCrunch Registry | NIPY Community | 2026-10-31 12:15:55 | 27 | ||||
|
PIA Resource Report Resource Website |
PIA (RRID:SCR_013267) | PIA | software resource | A prefix indexing and alignment software for next-generation sequencing (NGS) for whole human genome. | next-generation sequencing |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00676 | SCR_013267 | SciCrunch Registry | 2026-10-31 12:15:53 | 0 | |||||||||
|
miRSeqNovel Resource Report Resource Website 1+ mentions |
miRSeqNovel (RRID:SCR_013257) | miRSeqNovel | software resource | An R/Bioconductor based workflow for novel miRNA prediction from deep sequencing data. |
is listed by: OMICtools has parent organization: SourceForge |
Free, Public, Non-commercial | OMICS_00381 | SCR_013257 | SciCrunch Registry | 2026-10-31 12:15:57 | 2 | |||||||||
|
DynamicProg Resource Report Resource Website 1+ mentions |
DynamicProg (RRID:SCR_013217) | DynamicProg | software resource | A model-based statistical methods for base calling in Illumina''s next-generation sequencing platforms. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01150 | SCR_013217 | SciCrunch Registry | 2026-10-31 12:15:52 | 1 | ||||||||||
|
BEADS Resource Report Resource Website 10+ mentions |
BEADS (RRID:SCR_013229) | BEADS | software resource | Software for a normalization scheme that corrects nucleotide composition bias, mappability variations and differential local DNA structural effects in deep sequencing data. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: University of Cambridge; Cambridge; United Kingdom |
PMID:21646344 | OMICS_00466, biotools:beads | https://bio.tools/beads | SCR_013229 | SciCrunch Registry | BEADS: Bias Elimination Algorithm for Deep Sequencing, Bias Elimination Algorithm for Deep Sequencing | 2026-10-31 12:15:56 | 38 | ||||||
|
CongrPE Resource Report Resource Website 1+ mentions |
CongrPE (RRID:SCR_013190) | CongrPE | software resource | A de novo assembly algorithm for Next-Generation Sequencing technology. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00011 | SCR_013190 | SciCrunch Registry | 2026-10-31 12:15:52 | 1 | ||||||||||
|
CallSim Resource Report Resource Website |
CallSim (RRID:SCR_013192) | CallSim | software resource | A software application that provides evidence for the validity of base calls believed to be sequencing errors and it is applicable to Ion Torrent and 454 data. | matlab |
is listed by: OMICtools has parent organization: SourceForge |
Apache License | OMICS_01098 | SCR_013192 | SciCrunch Registry | CallSim - Low-volume read processing base corrector | 2026-10-31 12:16:00 | 0 | |||||||
|
SAPAS Resource Report Resource Website 50+ mentions |
SAPAS (RRID:SCR_013195) | SAPAS | software resource | A RNA-seq method for polyA research. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01413 | SCR_013195 | SciCrunch Registry | 2026-10-31 12:15:52 | 68 | ||||||||||
|
ArrayOligoSelector Resource Report Resource Website 10+ mentions |
ArrayOligoSelector (RRID:SCR_013494) | ArrayOligoSelector | software resource | Software program to systematically design gene specific long oligonucleotide probes for entire genomes, for the purpose of developing whole genome microarrays. For each open reading frame, the program optimizes the oligo selection based upon several parameters, including uniqueness in the genome, sequence complexity, lack of self-binding, GC content and proximity to the 3''end of the gene. |
is listed by: OMICtools has parent organization: University of California at San Francisco; California; USA has parent organization: SourceForge |
PMID:12620119 | Free, Public, Commercial requires license, Use of the blat or gfclient options requires license | OMICS_00826 | SCR_013494 | SciCrunch Registry | 2026-10-31 12:15:56 | 13 | ||||||||
|
Dissect Resource Report Resource Website |
Dissect (RRID:SCR_000058) | Dissect | alignment software, data processing software, image analysis software, software application, software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software transcriptome-to-genome alignment tool, which can identify and characterize transcriptomic events such as duplications, inversions, rearrangements and fusions. | Structural events containing transcripts, transcriptome-to-genome alignment, identify and characterize transcriptomic events, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge has parent organization: Simon Fraser University; British Columbia; Canada |
PMID:22689759 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01346, biotools:dissect | https://bio.tools/dissect | SCR_000058 | SciCrunch Registry | Dissect: DIScovery of Structural Events Containing Transcripts, DIScovery of Structural Events Containing Transcripts | 2026-10-31 12:18:27 | 0 | |||||
|
Biologic Stylus Resource Report Resource Website |
Biologic Stylus (RRID:SCR_002991) | Biologic Stylus | simulation software, software application, software resource, source code | Biologic Stylus is Biologic Institute's Stylus simulation software suite. Programming Language: C++, Python | bioinformatics, simulation | has parent organization: SourceForge | Free, Available for download, Freely available | nif-0000-30198 | SCR_002991 | SciCrunch Registry | biologicstylus | 2026-10-31 12:18:26 | 0 |
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