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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Shimmer Resource Report Resource Website |
Shimmer (RRID:SCR_001164) | software resource | Software package that detects somatic single-nucleotide variants using statistical hypothesis testing with multiple testing correction. It uses Fisher's exact test along with multiple testing correction (Benjamini-Hochberg) to find significant differences between allele composition with a specified false discovery rate. | standalone software, bam |
is listed by: OMICtools has parent organization: National Human Genome Research Institute |
PMID:23620360 | Free, Available for download, Freely available | OMICS_03612 | SCR_001164 | 2026-08-01 12:01:33 | 0 | ||||||||
|
DiMO Resource Report Resource Website 1+ mentions |
DiMO (RRID:SCR_001168) | DiMO | software resource | Software for discriminative motif optimization based on perceptron training. It takes a seed motif along with a positive and a negative database and improves the motif based on a discriminative strategy. They use the area under receiver-operating characteristic curve (AUC) as a measure of discriminating power of motifs and a strategy based on perceptron training that maximizes AUC rapidly in a discriminative manner. | r, motif, perceptron |
is listed by: OMICtools has parent organization: Washington University in St. Louis; Missouri; USA |
PMID:24369152 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02190 | SCR_001168 | Discriminative Motif Optimizer, DiMO: Discriminative Motif Optimizer | 2026-08-01 12:01:33 | 1 | ||||||
|
ExomePeak Resource Report Resource Website 1+ mentions |
ExomePeak (RRID:SCR_001076) | exomePeak | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. Software package developed for the analysis of affinity-based epitranscriptome shortgun sequencing data from MeRIP-seq (maA-seq). It was built on the basis of the exomePeak MATLAB package with new functions for differential analysis of two experimental conditions to unveil the dynamics in post-transcriptional regulation of the RNA methylome. The exomePeak R-package accepts and statistically supports multiple biological replicates, internally removes PCR artifacts and multi-mapping reads, outputs exome-based binding sites (RNA methylation sites) and detects differential post-transcriptional RNA modification sites between two experimental conditions in term of percentage rather the absolute amount. | r, matlab |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: University of Texas at San Antonio; Texas; USA |
PMID:23589649 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00570 | SCR_001076 | 2026-08-01 12:01:22 | 4 | |||||||
|
ParticleCall Resource Report Resource Website |
ParticleCall (RRID:SCR_001103) | ParticleCall | software resource | A base-calling algorithm for Illumina DNA sequencing. | illumina |
is listed by: OMICtools has parent organization: SourceForge |
PMID:22776067 | OMICS_01154 | SCR_001103 | 2026-08-01 12:01:23 | 0 | ||||||||
|
Google Compute Engine Resource Report Resource Website 1+ mentions |
Google Compute Engine (RRID:SCR_001011) | Compute Engine | service resource | An infrastructure as a service that lets you run your large-scale computing workloads on Linux virtual machines hosted on Google's infrastructure. | cloud | is listed by: OMICtools | OMICS_01204 | SCR_001011 | 2026-08-01 12:01:29 | 2 | |||||||||
|
CUDA-EC Resource Report Resource Website 1+ mentions |
CUDA-EC (RRID:SCR_001090) | CUDA-EC | software resource | A fast parallel error correction tool for short reads. | c, gpu/cuda, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:20426693 | Free, Available for download, Freely available | OMICS_01100, biotools:cuda-ec | https://bio.tools/cuda-ec | SCR_001090 | Compute Unified Device Architecture | 2026-08-01 12:01:31 | 1 | |||||
|
qips Resource Report Resource Website |
qips (RRID:SCR_001092) | qips | software resource | A software package for analyzing ChIP-seq (Chromatin ImmunoPrecipitation on sequencing) data that finds enriched regions of arbitrary lengths and is therefore especially suited for analyzing ChIP-seq of histone marks or polymerase. | command-line, c++, python |
is listed by: OMICtools has parent organization: SourceForge |
Free, Available for download, Freely available | OMICS_00457 | SCR_001092 | 2026-08-01 12:01:39 | 0 | ||||||||
|
JBrowse Resource Report Resource Website 10+ mentions |
JBrowse (RRID:SCR_001004) | JBrowse | software resource | A high-performance visualization tool for interactive exploration of large, integrated genomic datasets written primarily in JavaScript. It supports a wide variety of data types, including array-based and next-generation sequence data, and genomic annotations. | genome |
is used by: Genome Resources for Yeast Chromosomes is listed by: OMICtools is listed by: Debian has parent organization: Broad Institute |
NHGRI 5R01HG004483-09 | PMID:22517427 PMID:21221095 |
GNU Lesser General Public License, Account required | OMICS_00918 | https://sources.debian.org/src/jbrowse/ | SCR_001004 | 2026-08-01 12:01:29 | 32 | |||||
|
flowWorkspace Resource Report Resource Website 1+ mentions |
flowWorkspace (RRID:SCR_001155) | software resource | Software package that facilitates comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis. | software package, mac os x, unix/linux, windows, r, data import, data representation, flow cytometry, preprocessing |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23020243 | Free, Available for download, Freely available | OMICS_05616 | SCR_001155 | flowWorkspace - Import flowJo Workspaces into BioConductor and replicate flowJo gating with flowCore | 2026-08-01 12:01:40 | 3 | |||||||
|
GimmeMotifs Resource Report Resource Website 1+ mentions |
GimmeMotifs (RRID:SCR_001146) | GimmeMotifs | software resource | Software that provides a de novo motif prediction pipeline, especially suited for ChIP-seq datasets. It incorporates several existing motif prediction algorithms in an ensemble method to predict motifs and clusters these motifs using the WIC similarity scoring metric., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | linux, chip-seq, motif, cluster, python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Radboud University; Nijmegen; The Netherlands |
PMID:21081511 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:gimmemotifs, OMICS_02150 | https://bio.tools/gimmemotifs | SCR_001146 | GimmeMotifs: a systematic de novo motif prediction pipeline | 2026-08-01 12:01:23 | 4 | |||||
|
ArrayExpress (R) Resource Report Resource Website 1+ mentions |
ArrayExpress (R) (RRID:SCR_000120) | ArrayExpress (R) | software resource | Software to access the ArrayExpress Repository at EBI and build Bioconductor data structures: ExpressionSet, AffyBatch, NChannelSet | microarray |
is listed by: OMICtools is related to: ArrayExpress has parent organization: Bioconductor has parent organization: European Bioinformatics Institute |
PMID:19505942 | Free, Available for download, Freely available | OMICS_01974 | SCR_000120 | 2026-08-01 12:01:09 | 1 | |||||||
|
D-Tailor Resource Report Resource Website |
D-Tailor (RRID:SCR_000115) | software resource | A fully extendable software framework, for property-based design of synthetic DNA sequences. | standalone software, python |
is listed by: OMICtools has parent organization: SourceForge |
PMID:24398007 | Free, Available for download, Freely available | OMICS_04768 | SCR_000115 | DNA-Tailor | 2026-08-01 12:01:08 | 0 | |||||||
|
AffyRNADegradation Resource Report Resource Website |
AffyRNADegradation (RRID:SCR_000118) | AffyRNADegradation | software resource | Software package that helps with the assessment and correction of RNA degradation effects in Affymetrix 3' expression arrays. The parameter d gives a robust and accurate measure of RNA integrity. The correction removes the probe positional bias, and thus improves comparability of samples that are affected by RNA degradation. | rna degradation, gene expression, microarray, preprocessing, affymetrix, rna, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor has parent organization: University of Leipzig; Saxony; Germany |
PMID:23097420 | Free, Available for download, Freely available | OMICS_01975, biotools:affyrnadegradation | https://bio.tools/affyrnadegradation | SCR_000118 | 2026-08-01 12:01:08 | 0 | ||||||
|
SnowsShoes-FTD Resource Report Resource Website |
SnowsShoes-FTD (RRID:SCR_000076) | SnowsShoes-FTD | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 18,2023. A free bioinformatics software tool to help identify fusion transcripts from paired-end transcriptome sequencing data. The source codes of SnowShoes-FTD are provided in two formats: one configured to run on the Sun Grid Engine for parallelization with shorter run time, and the other formatted to run on a single LINUX node. | software, bioinformatics, transcriptome sequences, data, LINUX, node, free |
is listed by: OMICtools has parent organization: Mayo Clinic |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01356 | SCR_000076 | 2026-08-01 12:01:08 | 0 | ||||||||
|
VariantAnnotation Resource Report Resource Website 1+ mentions |
VariantAnnotation (RRID:SCR_000074) | VariantAnnotation | software resource | Software package to annotate variants, compute amino acid coding changes, and predict coding outcomes. | annotation, genetic variant, data import, genetics, high throughput sequencing, snp, sequencing |
is listed by: OMICtools is related to: CRAN has parent organization: Bioconductor has parent organization: Fred Hutchinson Cancer Center |
PMID:24681907 | Free, Available for download, Freely available | OMICS_02073 | SCR_000074 | VariantAnnotation - Annotation of Genetic Variants | 2026-08-01 12:01:07 | 8 | ||||||
|
SOAPfusion Resource Report Resource Website 1+ mentions |
SOAPfusion (RRID:SCR_000079) | SOAPfusion | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 22,2022. An open source software tool for fusion discovery with paired-end RNA-Seq reads. The tool follows a different strategy by finding fusions directly and verifying them, differentiating it from all other existing tools by finding the candidate regions and searching for the fusions afterwards. | software, open source, free, RNA, sequencing, data, computing, research, analysis, rna-seq, candidate regions, bio.tools |
is listed by: OMICtools is listed by: SOAP is listed by: bio.tools is listed by: Debian |
Guangdong Innovative Research Team Program ; General Research Fund of the Hong Kong Government |
PMID:24123671 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01358, biotools:soapfusion | https://bio.tools/soapfusion | SCR_000079 | 2026-08-01 12:01:08 | 3 | |||||
|
timecourse Resource Report Resource Website 1+ mentions |
timecourse (RRID:SCR_000077) | timecourse | software resource | Software functions for data analysis and graphical displays for developmental microarray time course data. | microarray, differential expression, time course, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: CRAN has parent organization: Bioconductor has parent organization: University of California at Berkeley; Berkeley; USA |
Free, Available for download, Freely available | OMICS_01980, biotools:timecourse | https://bio.tools/timecourse | SCR_000077 | timecourse - Statistical Analysis for Developmental Microarray Time Course Data | 2026-08-01 12:01:07 | 5 | ||||||
|
Patchwork Resource Report Resource Website 1+ mentions |
Patchwork (RRID:SCR_000072) | Patchwork | software resource | Software tool for analyzing and visualizing allele-specific copy numbers and loss-of-heterozygosity in cancer genomes. The data input is in the format of whole-genome sequencing data which enables characterization of genomic alterations ranging in size from point mutations to entire chromosomes. High quality results are obtained even if samples have low coverage, ~4x, low tumor cell content or are aneuploid. Patchwork takes BAM files as input whereas PatchworkCG takes input from CompleteGenomics files. TAPS performs the same analysis as Patchwork but for microarray data. | genome, allele, copy number, bam, unix, r, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Uppsala University; Uppsala; Sweden |
Cancer, Tumor | PMID:23531354 | Free, Available for download, Freely available | biotools:patchwork, OMICS_02118 | https://bio.tools/patchwork | SCR_000072 | 2026-08-01 12:01:09 | 9 | |||||
|
TACOA Resource Report Resource Website |
TACOA (RRID:SCR_000107) | TACOA | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 31,2025. Software that can accurately predict the taxonomic origin of genomic fragments from metagenomic data sets by combining the advantages of the k -NN approach with a smoothing kernel function. | taxonomy, genomic fragment, metagenome |
is listed by: OMICtools has parent organization: Bielefeld University; North Rhine-Westphalia; Germany |
PMID:19210774 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01467 | SCR_000107 | 2026-08-01 12:01:10 | 0 | |||||||
|
Tablet Resource Report Resource Website 1+ mentions |
Tablet (RRID:SCR_000017) | Tablet | software resource | A lightweight, high-performance graphical viewer for next generation sequence assemblies and alignments. | next generation sequence, assembly, alignment |
is listed by: OMICtools has parent organization: James Hutton Institute; Scotland; United Kingdom |
PMID:22445902 | Free, Available for download, Freely available | OMICS_00896 | SCR_000017 | Tablet - Next Generation Sequence Assembly Visualization | 2026-08-01 12:01:06 | 8 |
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