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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Micro-Analyzer Resource Report Resource Website |
Micro-Analyzer (RRID:SCR_000394) | Micro-Analyzer | software resource | Java tool that performs the preprocessing of Expression and SNPs microarray Affymetrix. The software allows the automatic download and the use of the clustering and visualization software as the Mev 4.0. The tool is equipped by a graphical interface (Swing) that allows to the user to: Create the workspace (files .cel, preferred algorithms , output, libraries to use); Run/save analysis and workspace settings (xml); Efficient download of the libraries (http, ftp, MD5); Customize basic and graphical settings (objects serialization and deserialization). Type of SNPs: Mapping 500k or preceding chips, SNP 5.0, SNP 6.0. Available for 32 or 64 bit systems, and for Windows and Linux Systems. | windows, linux, java, java swing, gene expression, snp, microarray, affymetrix, preprocessing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:23731720 | Free, Available for download, Freely available | OMICS_01919, biotools:microanalyzer | https://bio.tools/microanalyzer | SCR_000394 | SciCrunch Registry | microAnalyzer | 2026-10-10 12:35:35 | 0 | |||||
|
FunctSNP Resource Report Resource Website |
FunctSNP (RRID:SCR_000393) | FunctSNP | software resource | An R package for linking SNPs (Single Nucleotide Polymorphisms) to functional knowledge. | single nucleotide polymorphism |
is listed by: OMICtools has parent organization: SourceForge |
PMID:20534127 | Free, Available for download, Freely available | OMICS_01925 | SCR_000393 | SciCrunch Registry | FunctSNP - Linking SNPs to functional knowledge | 2026-10-10 12:35:34 | 0 | ||||||
|
flowStats Resource Report Resource Website 1+ mentions |
flowStats (RRID:SCR_000399) | software resource | Software using statistical methods and functionality to analyze flow data that is beyond the basic infrastructure provided by the flowCore package. | software package, mac os x, unix/linux, windows, r, cell based assay, flow cytometry |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_05611 | SCR_000399 | SciCrunch Registry | flowStats - Statistical methods for the analysis of flow cytometry data | 2026-10-10 12:35:37 | 1 | ||||||||
|
d2-tools Resource Report Resource Website |
d2-tools (RRID:SCR_000425) | software resource | Software toolbox for counting the frequency of K-tuple from sequencing datasets and calculate the dissimilarity. | standalone software, python, r |
is listed by: OMICtools has parent organization: Google Code |
PMID:24392128 | Free, Freely available | OMICS_02621 | SCR_000425 | SciCrunch Registry | 2026-10-10 12:35:37 | 0 | ||||||||
|
PyMOL Resource Report Resource Website 1000+ mentions |
PyMOL (RRID:SCR_000305) | 3d visualization software, data processing software, data visualization software, software application, software resource | A user-sponsored molecular visualization software system on an open-source foundation. The software has the capabilities to view, render, animate, export, present and develop three dimensional molecular structures. | visualization, molecule, 3d, molecular structure visualization, molecular visualization system, |
is listed by: Debian is listed by: OMICtools is listed by: SoftCite |
Restricted | nlx_156834, OMICS_03802 | https://sources.debian.org/src/pymol/ | SCR_000305 | SciCrunch Registry | 2026-10-10 12:35:33 | 3493 | ||||||||
|
Clonality Resource Report Resource Website |
Clonality (RRID:SCR_000293) | Clonality | software resource | Software package for clonality testing providing statistical tests for clonality versus independence of tumors from the same patient based on their loss of heterozygosity (LOH) or genomewide copy number profiles. | classification, copy number variant, microarray, acgh |
is listed by: OMICtools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02059 | SCR_000293 | SciCrunch Registry | Clonality - Clonality testing | 2026-10-10 12:35:32 | 0 | |||||||
|
LIPAGE Resource Report Resource Website 1+ mentions |
LIPAGE (RRID:SCR_000290) | data management software, software application, software resource | Laboratory information management system for proteomics. The software works with 2DPAGE-based proteomics workflow. | proteomics, laboratory, open source, 2dpage, management system |
is listed by: OMICtools has parent organization: SourceForge |
PMID:17018156 | Free, Available for download, Freely available | OMICS_02553 | SCR_000290 | SciCrunch Registry | LIMS for proteomics | 2026-10-10 12:35:34 | 1 | |||||||
|
RADtools Resource Report Resource Website 1+ mentions |
RADtools (RRID:SCR_000324) | software resource | Software tools for processing RAD Sequencing Illumina reads. Version 1.0 is a pipeline for transforming Illumina reads into candidate genetic markers. | standalone software, illumina | is listed by: OMICtools | PMID:21541297 | Free, Available for download, Freely available | OMICS_03727 | https://www.wiki.ed.ac.uk/display/RADSequencing/ | SCR_000324 | SciCrunch Registry | 2026-10-10 12:35:35 | 1 | |||||||
|
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 | SciCrunch Registry | 2026-10-10 12:35:30 | 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 | SciCrunch Registry | DNA-Tailor | 2026-10-10 12:35:29 | 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 | SciCrunch Registry | 2026-10-10 12:35:29 | 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 | SciCrunch Registry | 2026-10-10 12:35:28 | 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 | SciCrunch Registry | VariantAnnotation - Annotation of Genetic Variants | 2026-10-10 12:35:28 | 9 | ||||||
|
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 |
General Research Fund of the Hong Kong Government ; Guangdong Innovative Research Team Program |
PMID:24123671 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01358, biotools:soapfusion | https://bio.tools/soapfusion | SCR_000079 | SciCrunch Registry | 2026-10-10 12:35:28 | 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 | SciCrunch Registry | timecourse - Statistical Analysis for Developmental Microarray Time Course Data | 2026-10-10 12:35:28 | 5 | ||||||
|
Patchwork Resource Report Resource Website 10+ 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 | SciCrunch Registry | 2026-10-10 12:35:28 | 10 | |||||
|
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 | SciCrunch Registry | 2026-10-10 12:35:29 | 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 | SciCrunch Registry | Tablet - Next Generation Sequence Assembly Visualization | 2026-10-10 12:35:27 | 8 | ||||||
|
AutoPrime Resource Report Resource Website 1+ mentions |
AutoPrime (RRID:SCR_000097) | AutoPrime | data access protocol, software resource, web service | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Server to rapidly design primers for real-time PCR measurement of eukaryotic expression. | primer, real-time pcr, primer design |
is listed by: OMICtools has parent organization: German Cancer Research Center |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02333 | SCR_000097 | SciCrunch Registry | 2026-10-10 12:35:29 | 7 | ||||||||
|
siRNArules Resource Report Resource Website |
siRNArules (RRID:SCR_000096) | software resource | An open-source JAVA program that is surprisingly efficient at predicting active siRNAs. | standalone software, java |
is listed by: OMICtools has parent organization: SourceForge |
PMID:16870995 | Free, Available for download, Freely available | OMICS_04742 | SCR_000096 | SciCrunch Registry | 2026-10-10 12:35:29 | 0 |
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