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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
Nestly Resource Report Resource Website |
Nestly (RRID:SCR_003472) | Nestly | software resource | A Python package to facilitate running tools with nested combinations of parameters and inputs. It provides three components: a module to build nested directory structures corresponding to choices of parameters; the nestrun script to run a given command using each set of parameter choices; the nestagg script to aggregate results of the individual runs into a CSV file, as well as support for more complex aggregation. Also included is a module for easily specifying nested dependencies for the SCons build tool, enabling incremental builds. | python | is listed by: OMICtools | PMID:23220574 | MIT License | OMICS_02300 | SCR_003472 | 2026-07-25 12:05:40 | 0 | |||||||
|
PoPoolation Resource Report Resource Website 100+ mentions |
PoPoolation (RRID:SCR_003495) | PoPoolation | software resource | A collection of tools to facilitate population genetic studies of next generation sequencing data from pooled individuals. It builds upon open source tools (bwa, samtools) and uses standard file formats (gtf, sam, pileup) to ensure a wide compatibility. PoPoolation allows to calculate Tajima's Pi, Watterson's Theta and Tajima's D for reference sequences using a sliding window approach. Alternatively these population genetic estimators may be calculated for a set of genes (provided as gtf). One of the main challenges in population genomics is to identify regions of intererest on a genome wide scale. PoPoolation will greatly aid this task by allowing a fast and user friendly analysis of NGS data from DNA pools. | population genetics, next generation sequencing, sliding window, genome, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:21253599 | Acknowledgement requested | OMICS_04414, biotools:popoolation | https://bio.tools/popoolation | SCR_003495 | 2026-07-25 12:05:40 | 139 | ||||||
|
JISTIC Resource Report Resource Website 1+ mentions |
JISTIC (RRID:SCR_003482) | JISTIC | software resource | Software tool for analyzing datasets of genome-wide copy number variation to identify driver aberrations in cancer. | copy number variation, candidate gene, gene |
is listed by: OMICtools has parent organization: Columbia University; New York; USA |
Cancer | PMID:20398270 | Free, Public | OMICS_02297 | SCR_003482 | 2026-07-25 12:05:40 | 2 | ||||||
|
MetABEL Resource Report Resource Website 1+ mentions |
MetABEL (RRID:SCR_003429) | MetABEL | software resource | Software for meta-analysis of genome-wide SNP association results. | is listed by: OMICtools | PMID:17384015 | Free, Available for download, Freely available | OMICS_00237 | https://www.rdocumentation.org/packages/MetABEL/versions/0.2-0 | SCR_003429 | 2026-07-25 12:05:39 | 6 | |||||||
|
LaSSO Resource Report Resource Website 100+ mentions |
LaSSO (RRID:SCR_003418) | software resource | An R script that creates a FASTA database containing all possible lariat signatures from a given set of introns. | standalone software, r, FASEB list | is listed by: OMICtools | PMID:24709818 | Free, Available for download, Freely available | OMICS_04622 | SCR_003418 | Lariat Sequence Site Origin | 2026-07-25 12:05:40 | 157 | |||||||
|
metaphor Resource Report Resource Website 100+ mentions |
metaphor (RRID:SCR_003450) | metaphor | software resource | A free and open-source add-on for conducting meta-analyses with the statistical software environment R. | is listed by: OMICtools | GNU General Public License, v2 | OMICS_00240 | SCR_003450 | The metafor package, The metafor package: A meta-analysis package for R | 2026-07-25 12:05:41 | 311 | ||||||||
|
SWAN Resource Report Resource Website 100+ mentions |
SWAN (RRID:SCR_003455) | SWAN | software resource | Software that improves the results from the Illumina infinium HumanMethylation450 BeadChips by reducing technical variation within and between arrays. SWAN is available in the minfi Bioconductor package. | dna methylation, microarray |
is listed by: OMICtools is related to: minfi has parent organization: Bioconductor |
PMID:22703947 | Free, Available for download, Freely available | OMICS_02303 | SCR_003455 | Subset-quantile Within Array Normalization | 2026-07-25 12:05:41 | 190 | ||||||
|
BMIQ Resource Report Resource Website 100+ mentions |
BMIQ (RRID:SCR_003446) | BMIQ | software resource | Software using a beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data. | illumina infinium 450k, dna methylation, probe design, normalization |
is listed by: OMICtools has parent organization: Google Code |
PMID:23175756 | Free, Available for download, Freely available | OMICS_02304 | https://aeteschendorff-lab.github.io/software/BMIQ/ | SCR_003446 | bmiq - Beta Mixture Quantile Model, Beta MIxture Quantile dilation | 2026-07-25 12:05:40 | 125 | |||||
|
GEPAT Resource Report Resource Website 1+ mentions |
GEPAT (RRID:SCR_003597) | GEPAT | software resource | A web-based software tool offering an integrated analysis of transcriptome data under genomic, proteomic and metabolic context. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:17543125 | OMICS_00765, biotools:gepat | https://bio.tools/gepat | SCR_003597 | Genome Expression Pathway Analysis Tool | 2026-07-25 12:05:41 | 2 | ||||||
|
Osprey Resource Report Resource Website 10+ mentions |
Osprey (RRID:SCR_003627) | Osprey | software resource | Oligonucleotide design software that calculates optimal oligonucleotides for a range of tasks: sequence assembly, differential expression, and microarrays (cDNA and spotted oligos)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. |
is listed by: OMICtools has parent organization: University of Calgary; Alberta; Canada |
PMID:15456895 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00832 | SCR_003627 | Osprey: Oligonucleotide Design Software | 2026-07-25 12:05:41 | 47 | |||||||
|
UEA sRNA toolkit Resource Report Resource Website 10+ mentions |
UEA sRNA toolkit (RRID:SCR_003620) | UEA sRNA toolkit | software resource | Software tools for the analysis of high-throughput small RNA data. | is listed by: OMICtools | PMID:22628521 | OMICS_00369 | SCR_003620 | 2026-07-25 12:05:42 | 32 | |||||||||
|
RINS Resource Report Resource Website 10+ mentions |
RINS (RRID:SCR_003652) | RINS | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on January 6, 2023. An intersection-based pathogen detection workflow that utilizes a user-provided custom reference genome set for identification of nonhuman sequences in deep sequencing datasets. This is a package recommended for advanced users only. | virus, rna-seq, dna-seq, viral integration, clipped-sequence, paired-end, reconstruction, fusion transcript, sequence, perl |
is listed by: OMICtools has parent organization: Stanford University School of Medicine; California; USA |
PMID:22377895 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00223 | SCR_003652 | 2026-07-25 12:05:41 | 26 | |||||||
|
J-Express Resource Report Resource Website 50+ mentions |
J-Express (RRID:SCR_003609) | J-Express | software resource | Gene expression analysis software using Java. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian is parent organization of: Mini Analysis Guide for Microarrays |
PMID:11301307 | Acknowledgement requested | biotools:j-express, OMICS_00767 | https://bio.tools/j-express | SCR_003609 | J-Express: Gene expression analysis software | 2026-07-25 12:05:41 | 86 | |||||
|
JATAC Resource Report Resource Website |
JATAC (RRID:SCR_003978) | JATAC | software resource | Software program for filtering duplicate 454 sequences by comparing flowgram information. | is listed by: OMICtools | PMID:23376350 | OMICS_01055 | SCR_003978 | 2026-07-25 12:05:45 | 0 | |||||||||
|
Quantitative Enrichment of Sequence Tags Resource Report Resource Website 10+ mentions |
Quantitative Enrichment of Sequence Tags (RRID:SCR_004065) | QuEST | software resource | A Kernel Density Estimator-based package for analysis of massively parallel sequencing data from chromatin immunoprecipitation (ChIP-seq) experiments. | genome-wide, transcription factor binding site, chip-seq, transcription factor, binding site, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: Stanford University; Stanford; California |
PMID:19160518 | OMICS_00458, biotools:quest | https://bio.tools/quest | SCR_004065 | Quantitative Enrichment of Sequence Tags: QuEST | 2026-07-25 12:05:46 | 49 | ||||||
|
Pash 3.0 Resource Report Resource Website 1+ mentions |
Pash 3.0 (RRID:SCR_004078) | Pash 3.0 | software resource | Performs sequence comparison and read mapping and can be employed as a module within diverse configurable analysis pipelines, including ChIP-Seq and methylome mapping by whole-genome bisulfite sequencing. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:21092284 | biotools:pash, OMICS_00586 | https://bio.tools/pash | SCR_004078 | 2026-07-25 12:05:46 | 1 | |||||||
|
GenGIS Resource Report Resource Website 10+ mentions |
GenGIS (RRID:SCR_001465) | software resource | A bioinformatics application that allows users to combine digital map data with information about biological sequences collected from the environment. It provides a 3D graphical interface in which the user can navigate and explore the data, as well as a Python interface that allows easy scripting of statistical analyses using the Rpy libraries. | standalone software | is listed by: OMICtools | Genome Atlantic ; Genome Canada ; Biomonitoring 2.0 Project ; Dalhousie Centre for Comparative Genomics and Evolutionary Bioinformatics ; Tula Foundation ; Natural Sciences and Engineering Research Council of Canada ; Dalhousie Faculty of Computer Science |
PMID:23922841 | Free, Available for download, Freely available | OMICS_04013 | http://kiwi.cs.dal.ca/GenGIS/ | SCR_001465 | 2026-07-25 12:05:03 | 38 | ||||||
|
ACME Resource Report Resource Website 50+ mentions |
ACME (RRID:SCR_001464) | ACME | software resource | A set of tools for analysing tiling array ChIP/chip, DNAse hypersensitivity, or other experiments that result in regions of the genome showing enrichment. It does not rely on a specific array technology (although the array should be a tiling array), is very general (can be applied in experiments resulting in regions of enrichment), and is very insensitive to array noise or normalization methods. It is also very fast and can be applied on whole-genome tiling array experiments quite easily with enough memory. | microarray |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: National Institutes of Health |
PMID:16939795 | Free, Available for download, Freely available | OMICS_01976 | SCR_001464 | Algorithms for Calculating Microarray Enrichment | 2026-07-25 12:05:03 | 59 | ||||||
|
PyLOH Resource Report Resource Website 1+ mentions |
PyLOH (RRID:SCR_001511) | software resource | Software for deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity. The model resolves the identifiability problem by integrating two types of sequencing information - somatic copy number alterations and loss of heterozygosity - within an unified probabilistic framework. | standalone software, python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24695406 | Free, Available for download, Freely available | OMICS_03559, biotools:pyloh | https://bio.tools/pyloh | SCR_001511 | 2026-07-25 12:05:03 | 4 | |||||||
|
CoGAPS Resource Report Resource Website 10+ mentions |
CoGAPS (RRID:SCR_001479) | CoGAPS | software resource | Software that infers biological processes which are active in individual gene sets from corresponding microarray measurements. It achieves this inference by combining a MCMC matrix decomposition algorithm (GAPS) with a novel statistic inferring activity on gene sets. | gene expression, microarray |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: Johns Hopkins University; Maryland; USA |
PMID:20810601 | Free, Available for download, Freely available | OMICS_01973 | SCR_001479 | Coordinated Gene Activity in Pattern Sets | 2026-07-25 12:05:03 | 36 |
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