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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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seq2HLA Resource Report Resource Website 1+ mentions |
seq2HLA (RRID:SCR_001199) | seq2HLA | software resource | Software for obtaining an individualXs HLA class I and II type and expression using standard NGS (Next-generation sequencing) RNA-Seq data. It comprises mapping RNA-Seq reads against a reference database of HLA alleles, determining and reporting HLA type, confidence score and locus-specific expression level. | illumina, next-generation sequencing, rna-seq, hla, hla allele, hla typing |
is listed by: OMICtools has parent organization: Johannes Gutenberg University Mainz; Rhineland-Palatinate; Germany |
BMBF | PMID:23259685 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02152 | SCR_001199 | seq2HLA - HLA typing from RNA-Seq sequence reads | 2026-08-15 11:22:03 | 3 | |||||
|
Sequedex Resource Report Resource Website 1+ mentions |
Sequedex (RRID:SCR_001233) | Sequedex | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025.Software to classify the function and phylogeny of reads as short as 30 bp. It is flexible, which can utilize multiple data modules and downstream analysis scripts. It is fast, reading in signature lists of 5-500 million peptide signatures in 1-15 minutes, and subsequently processes genomic fragments at the rate of 6 Gbp/hr. It parallelizes without significant increase in memory requirements until I/O bound on multiple input files; parallelization works well on 64 processors. | phylogenetic, function, profile, metagenomics, synthetic, dna sequence, classification, java, linux, mac os, genomic analysis, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Los Alamos National Laboratory |
PMID:22925230 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02110, biotools:sequedex | https://bio.tools/sequedex | SCR_001233 | 2026-08-15 11:22:03 | 1 | ||||||
|
Peking University; Beijing; China Resource Report Resource Website 1+ mentions |
Peking University; Beijing; China (RRID:SCR_001193) | PKU | commercial organization | Chinese research university in Beijing, China that offers undergraduate and graduate degree programs in pure and applied sciences, social sciences and humanities, and sciences of management and education. | chinese, research, public, applied science, basic science, management, education, social science, humanities |
is parent organization of: NTAP is parent organization of: MirSNP is parent organization of: Arabidopsis Hormone Database is parent organization of: ProTISA is parent organization of: Database of Rice Transcription Factors is parent organization of: Knowledgebase for Addiction Related Genes is parent organization of: Coding Potential Calculator is parent organization of: PLANTTFDB is parent organization of: SynDB: Synapse DataBase is parent organization of: SpliceDisease is parent organization of: KOBAS is parent organization of: AutismKB is parent organization of: Database of Poplar Transcription Factors is parent organization of: Database of Arabidopsis Transcription Factors is parent organization of: Chinese Longitudinal Healthy Longevity Survey (CLHLS) is parent organization of: Leaf Senescence Database is parent organization of: OKCAM: Ontology-based Knowledgebase for Cell Adhesion Molecules is parent organization of: SAPRED is parent organization of: MAP is parent organization of: National Antisense Transcript Database is parent organization of: Secreted Protein Database is parent organization of: CAMO - Cell Adhesion Molecule Ontology is parent organization of: HomeoDB is parent organization of: TransmiR is parent organization of: Gene Expression Profiling Interactive Analysis is parent organization of: single cell RNA-seq Data Visualization and Analysis |
ISNI:0000 0001 2256 9319, grid.11135.37, Crossref funder ID:501100007937, Wikidata:Q16952, nlx_76213 | https://ror.org/02v51f717 | http://en.pku.edu.cn/ | SCR_001193 | PKU | 2026-08-15 11:21:53 | 1 | ||||||
|
PeakAnalyzer Resource Report Resource Website 1+ mentions |
PeakAnalyzer (RRID:SCR_001194) | PeakAnalyzer | software resource | A set of standalone software programs for the automated processing of any genomic loci, with an emphasis on datasets consisting of ChIP-derived signal peaks. The software is able to identify individual binding / modification sites from enrichment loci, retrieve peak region sequences for motif discovery, and integrate experimental data with different classes of annotated elements throughout the genome. PeakAnalyzer requires a peak file and a feature annotation file in BED or GTF format. Complete annotation files for the current builds of the human (HG19) and mouse (MM9) genomes are provided with the software distribution. | genome, chip, signal peak, binding site, modification site, enrichment loci, peak region, sequence, motif, chip-seq, chip-chip, c++, java, linux, mac os x, windows, bed, gtf, annotation, r, high-throughput sequencing, chromatin binding, modification loci, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: European Bioinformatics Institute |
PMID:20691053 | Free, Available for download, Freely available | biotools:peakanalyzer, OMICS_02156 | https://bio.tools/peakanalyzer | SCR_001194 | 2026-08-15 11:21:53 | 3 | ||||||
|
BreakSeq Resource Report Resource Website 1+ mentions |
BreakSeq (RRID:SCR_001186) | BreakSeq | software resource | Software for scanning reads from short-read sequenced genomes against a human breakpoint library to accurately identify structural variants (SVs). The library of breakpoints at nucleotide resolution were assembled from collating and standardizing ~2,000 published structural variants (SVs). For each breakpoint, its ancestral state (through comparison to primate genomes) was inferred and its mechanism of formation (e.g., nonallelic homologous recombination, NAHR). | structural variant, breakpoint, nucleotide, fasta, gff, bowtie, genomic variation, junction mapping, insertion sequence, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Yale University; Connecticut; USA |
PMID:20037582 | THIS RESOURCE IS NO LONGER IN SERVICE | biotools:breakseq, OMICS_02168 | https://bio.tools/breakseq | SCR_001186 | Breakpoint Library and BreakSeq | 2026-08-15 11:22:03 | 1 | |||||
|
Third Reviewer Resource Report Resource Website 1+ mentions |
Third Reviewer (RRID:SCR_001187) | data or information resource, portal, narrative resource | THIS RESOURCE IS NO LONGER IN SERVICE, documented on January 11, 2017. The Third Reviewer is a forum for scientists to share opinions about recently published research. Currently both microbiology and neuroscience papers in different journals are included. Third Reviewer allows anonymous commenting and provides a centralized location for commentary on papers from 11 major neuroscience venues. | THIS RESOURCE IS NO LONGER IN SERVICE | nif-0000-07741 | SCR_001187 | ThirdReviewer, The Third Reviewer | 2026-08-15 11:21:53 | 1 | ||||||||||
|
categoryCompare Resource Report Resource Website 1+ mentions |
categoryCompare (RRID:SCR_001223) | categoryCompare | data processing software, software application, data analysis software, software resource | A software package for meta-analysis of high-throughput experiments using feature annotations. It calculates significant annotations (categories) in each of two (or more) feature (i.e. gene) lists, determines the overlap between the annotations, and returns graphical and tabular data about the significant annotations and which combinations of feature lists the annotations were found to be significant. Interactive exploration is facilitated through the use of RCytoscape (heavily suggested). | annotation, go, gene expression, multiple comparison, pathway, gene |
uses: Cytoscape is listed by: OMICtools is related to: Gene Ontology is related to: CRAN has parent organization: Bioconductor |
PMID:24808906 | Free, Available for download, Freely available | OMICS_02122 | SCR_001223 | categoryCompare - Meta-analysis of high-throughput experiments using feature annotations | 2026-08-15 11:22:03 | 9 | ||||||
|
Covance Resource Report Resource Website 5000+ mentions |
Covance (RRID:SCR_001224) | Covance, CVD | commercial organization | A contract research organization providing drug development and animal testing services. Under the name Covance Research Products Inc., based in Denver, Pennsylvania, the company also deals in the import, breeding and sale of laboratory animals. It breeds dogs, rabbits, guinea pigs, non-human primates, and pigs, and runs the largest non-human primate laboratory in Germany. (Wikipedia) | drug development, drug, pharmaceutical, laboratory animal | nlx_152335, grid.469910.3, Wikidata: Q29123945 | https://ror.org/02phsd572 | SCR_001224 | Covance Research Products Inc., Covance Inc., Covance Research Products Inc | 2026-08-15 11:21:53 | 7527 | ||||||||
|
MergeMaid Resource Report Resource Website 1+ mentions |
MergeMaid (RRID:SCR_001221) | MergeMaid | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 18,2025. R extension whose functions are intended for cross-study comparison of gene expression array data. Required from the user is gene expression matrices, their corresponding gene-id vectors and other useful information, and they could be "list", "matrix", or "ExpressionSet". The main function is "mergeExprs" which transforms the input objects into data in the merged format, such that common genes in different datasets can be easily found. And the function "intcor" calculate the correlation coefficients. Other functions use the output from "modelOutcome" to graphically display the results and cross-validate associations of gene expression data with survival. | differential expression, microarray, visualization, gene expression |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:16646808 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02124 | SCR_001221 | Merge Maid | 2026-08-15 11:21:54 | 3 | ||||||
|
Microarray Data Analysis System Resource Report Resource Website 1+ mentions |
Microarray Data Analysis System (RRID:SCR_001218) | MIDAS | software resource | Application that provides users an interface to design analysis protocols combining one or more normalization and filtering steps. In this way, data from many individual hybridizations can be treated in a uniform and reproducible manner. | microarray, normalization, windows, mac osx, linux, java |
is listed by: OMICtools has parent organization: TM4 |
Artistic License | OMICS_02126 | https://sourceforge.net/projects/midas-tm4/ | http://www.tm4.org/midas.html | SCR_001218 | TM4 Microarray Software Suite: Microarray Data Analysis System, TM4 Microarray Software Suite: MIDAS, MIDAS (TM4 Microarray Software Suite), TM4 MIDAS, MIDAS: Microarray Data Analysis System | 2026-08-15 11:22:03 | 4 | |||||
|
globaltest Resource Report Resource Website 10+ mentions |
globaltest (RRID:SCR_001256) | globaltest | data processing software, software application, data analysis software, software resource, sequence analysis software | A software package that tests groups of covariates (or features) for association with a response variable. The package implements the test with diagnostic plots and multiple testing utilities, along with several functions to facilitate the use of this test for gene set testing of GO and KEGG terms. | differential expression, go, microarray, one channel, pathway, bio.tools |
uses: KEGG is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: Gene Ontology has parent organization: Bioconductor |
PMID:34046931 | Free, Available for download, Freely available | biotools:globaltest, OMICS_02084 | https://bio.tools/globaltest | SCR_001256 | 2026-08-15 11:21:54 | 31 | ||||||
|
snpStats: SnpMatrix and XSnpMatrix classes and methods Resource Report Resource Website 50+ mentions |
snpStats: SnpMatrix and XSnpMatrix classes and methods (RRID:SCR_001249) | snpStats | software resource | Software for classes and statistical methods for large single nucleotide polymorphism (SNP) association studies. | r, single nucleotide polymorphism, genetic variability, microarray |
is listed by: OMICtools has parent organization: Bioconductor has parent organization: University of Cambridge; Cambridge; United Kingdom |
PMID:16720584 | Free, Available for download, Freely available | OMICS_02091 | SCR_001249 | 2026-08-15 11:21:54 | 79 | |||||||
|
piCALL Resource Report Resource Website 1+ mentions |
piCALL (RRID:SCR_001242) | piCALL | software resource | Software to detect short insertion / deletion variants (and SNPs) from population sequence data, i.e. sequence reads generated from a population of individuals. It uses a probabilistic model to utilize sequence reads from a population of individuals to automatically account for context-specific sequencing errors associated with indels. piCALL is implemented in C for use on Linux platforms and can be applied to sequence data from different sequencing platforms. However, the method requires each individual in a dataset to be sequenced using the same platform. The reads for each individual should be aligned to the same reference genome sequence. Note that the program will not be able to call indels from individual sequence datasets or data from a small number of individuals. | c, genotyping, indel, population, high-throughput sequencing, insertion, deletion, variant, single nucleotide polymorphism, linux, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Scripps Research Institute |
PMID:21653520 | OMICS_02098, biotools:picall | https://bio.tools/picall | http://polymorphism.scripps.edu/~vbansal/software/piCALL/ | SCR_001242 | 2026-08-15 11:21:53 | 1 | ||||||
|
mapDamage Resource Report Resource Website 100+ mentions |
mapDamage (RRID:SCR_001240) | mapDamage | software resource | Software for tracking and quantifying DNA damage patterns among ancient DNA sequencing reads generated by Next-Generation Sequencing platforms. | python, r, illumina, windows, perl, dna damage, dna sequencing, next-generation sequencing, dna, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Copenhagen; Copenhagen; Denmark |
PMID:23613487 PMID:21659319 DOI:10.1093/bioinformatics/btt193 |
Free, Available for download, Freely available | OMICS_02099, biotools:mapdamage | https://bio.tools/mapdamage, https://sources.debian.org/src/mapdamage/ | SCR_001240 | mapDamage 2.0, mapDamage: tracking and quantifying damage patterns in ancient DNA sequences, mapDamage2.0 | 2026-08-15 11:21:54 | 395 | |||||
|
KMC Resource Report Resource Website 10+ mentions |
KMC (RRID:SCR_001245) | KMC | software resource | Software utility for counting k-mers (sequences of consecutive k symbols) in a set of reads from genome sequencing projects. It scans the raw reads and produces a compact representation of all non-unique reads accompanied with number of their occurrences. The algorithm implemented makes use mostly of disk space rather than RAM, which allows to use KMC even on rather typical personal computers. | c++, k-mer, genome sequencing, linux, windows, de bruijn graph |
is listed by: OMICtools is listed by: Debian has parent organization: Silesian University of Technology; Silesia; Poland |
PMID:23679007 DOI:10.1093/bioinformatics/btv022 |
Free, Available for download, Freely available | OMICS_02095 | https://sources.debian.org/src/kmc/ | SCR_001245 | KMC - K-mer Counter, K-mer Counter | 2026-08-15 11:22:03 | 10 | |||||
|
DSK Resource Report Resource Website 1+ mentions |
DSK (RRID:SCR_001246) | DSK | software resource | A k-mer counting software that can count k-mers of large Illumina datasets on laptops and desktop computers. | illumina, k-mer, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:23325618 | Free, Freely available | biotools:dsk, OMICS_02094 | https://bio.tools/dsk | SCR_001246 | disk streaming of k-mers, DSK: disk streaming of k-mers | 2026-08-15 11:21:53 | 1 | |||||
|
ChIP-seq Resource Report Resource Website 5000+ mentions |
ChIP-seq (RRID:SCR_001237) | ChIP-seq | software toolkit, data processing software, software application, data analysis software, software resource | Set of software modules for performing common ChIP-seq data analysis tasks across the whole genome, including positional correlation analysis, peak detection, and genome partitioning into signal-rich and signal-poor regions. The tools are designed to be simple, fast and highly modular. Each program carries out a well-defined data processing procedure that can potentially fit into a pipeline framework. ChIP-Seq is also freely available on a Web interface. | high-throughput sequencing, chromatin immuno precipitation, chip-seq, genome, c |
is listed by: OMICtools has parent organization: SourceForge has parent organization: Ecole Polytechnique Federale de Lausanne; Lausanne; Switzerland has parent organization: SIB Swiss Institute of Bioinformatics |
PMID:27863463 | Free, Available for download, Freely available | OMICS_02103 | https://epd.expasy.org/chipseq/, https://chip-seq.sourceforge.net/ | SCR_001237 | ChIP-seq - Tools for the analysis of ChIP-seq data | 2026-08-15 11:22:03 | 8035 | |||||
|
exomeCopy Resource Report Resource Website 10+ mentions |
exomeCopy (RRID:SCR_001276) | exomeCopy | software resource | Software package for detection of copy number variants (CNV) from exome sequencing samples, including unpaired samples. The package implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count. | copy number variation, genetics, sequencing, exome |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:23089826 | Free, Available for download, Freely available | OMICS_02062 | http://www.bioconductor.org/packages/release/bioc/html/exomeCopy.html | SCR_001276 | exomeCopy - Copy number variant detection from exome sequencing read depth | 2026-08-15 11:22:04 | 16 | |||||
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SMAP Resource Report Resource Website 100+ mentions |
SMAP (RRID:SCR_001270) | SMAP | software resource | Software package providing functions and classes for DNA copy number profiling of array-CGH data. | copy number variation, microarray, two channel |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:18204059 | Free, Available for download, Freely available | OMICS_02068 | SCR_001270 | SMAP - A Segmental Maximum A Posteriori Approach to Array-CGH Copy Number Profiling | 2026-08-15 11:22:04 | 210 | ||||||
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Local Ancestry in adMixed Populations Resource Report Resource Website 1+ mentions |
Local Ancestry in adMixed Populations (RRID:SCR_001258) | LAMP | software resource | A software package for the inference of locus-specific ancestry in recently admixed populations. LAMP-LD takes the genotypes of admixed individuals as well as reference haplotype panels approximating the mixing ancestral populations, and outputs the estimated number of alleles from each ancestry in each locus for each individual. The LAMP-LD package also includes the program LAMP-HAP, which processes haplotype data when high-quality phasing is available, and utilizes trio nuclear family designs to improve estimation accuracy. LAMP-LD is based on a window-based processing combined within a hierarchical Hidden Markov Model. It can process 2,3 or 5 mixing populations, and its short per-sample processing time makes it suitable for analyzing large datasets of dense SNP panels. The original program LAMP does not use the LD and therefore is not as accurate, but it is useful in cases where the SNP density is not high enough or when the ancestral haplotypes are unkown. | locus, ancestry, admixed, population, genotype, haplotype, allele | is listed by: OMICtools | NSF 513599 | PMID:22495753 PMID:19477991 PMID:18252211 |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02080 | SCR_001258 | 2026-08-15 11:21:54 | 9 |
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