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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
ALDEx2 Resource Report Resource Website 100+ mentions |
ALDEx2 (RRID:SCR_003364) | software resource | Software tool to examine compositional high-throughput sequence data with Welch's t-test. A differential relative count abundance analysis for the comparison of two conditions. For example, single-organism and meta-rna-seq high-throughput sequencing assays, or of selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected Benjamini-Hochberg false discovery rate given the biological and sampling variation using several parametric and non-parametric tests. Can to glm and Kruskal-Wallace tests on one-way ANOVA style designs. | standalone software, r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools is related to: aldex has parent organization: Western University; Ontario; Canada |
PMID:24910773 | GNU Affero General Public License, v3 | biotools:aldex2, OMICS_04634 | https://bio.tools/aldex2 | SCR_003364 | 2025-04-19 06:41:41 | 418 | |||||||
|
RCircos Resource Report Resource Website 100+ mentions |
RCircos (RRID:SCR_003310) | software resource | Software package that provides a simple and flexible way to generate Circos 2D track plot images for genomic data visualization. The types of plots include: heatmap, histogram, lines, scatterplot, tiles and plot items for further decorations include connector, link (lines and ribbons), and text (gene) label. All functions require only R graphics package that comes with R base installation. | standalone software, unix/linux, mac os x, windows, r |
is listed by: OMICtools is related to: shinyCircoss has parent organization: CRAN has parent organization: Bitbucket |
PMID:23937229 | GNU General Public License, v2, v3 | OMICS_04661 | https://bitbucket.org/henryhzhang/rcircos/ | SCR_003310 | RCircos: Circos 2D Track Plot | 2025-04-19 06:41:39 | 187 | ||||||
|
JCVI Primer Designer Resource Report Resource Website 1+ mentions |
JCVI Primer Designer (RRID:SCR_003275) | JCVI Primer Designer | software resource | High throughput PCR primer design software. Target regions defined through a rich set of descriptors, such as Ensembl accessions and arbitrary genomic coordinates, may be specified. Primer pairs are then selected computationally to produce a minimal amplicon set capable of tiling across the specified target regions. As part of the tiling process, primer pairs are computationally screened to meet the criteria for success with one of two PCR amplification protocols. | perl, command-line, pcr primer design, pcr, primer, high throughput sequencing |
is listed by: OMICtools has parent organization: SourceForge |
PMID:18405373 | GNU General Public License, v2 | OMICS_02330 | SCR_003275 | 2025-04-19 06:41:38 | 1 | |||||||
|
ddCt Resource Report Resource Website 100+ mentions |
ddCt (RRID:SCR_003396) | ddCt | software resource | Software package providing an approximation method to determine relative gene expression with quantitative real-time PCR (qRT-PCR) experiments. It requires no standard curve for each primer-target pair, therefore reducing the working load and yet returning accurate enough results as long as the assumptions of the amplification efficiency hold. The package implements a pipeline to collect, analyze and visualize qRT-PCR results, for example those from TaqMan SDM software, mainly using the ddCt method. The pipeline can be either invoked by a script in command-line or through the API consisting of S4-Classes, methods and functions. | differential expression, gene expression, microtitre plate assay, q-pcr |
is listed by: OMICtools has parent organization: Bioconductor |
GNU Lesser General Public License, v3 | OMICS_02312 | SCR_003396 | Delta-Delta-Ct | 2025-04-19 06:41:42 | 314 | |||||||
|
ggbio Resource Report Resource Website 10+ mentions |
ggbio (RRID:SCR_003313) | software resource | An R package for extending the grammar of graphics for genomic data. The graphics are designed to answer common scientific questions, in particular those often asked of high throughput genomics data. All core Bioconductor data structures are supported, where appropriate. The package supports detailed views of particular genomic regions, as well as genome-wide overviews. Supported overviews include ideograms and grand linear views. High-level plots include sequence fragment length, edge-linked interval to data view, mismatch pileup, and several splicing summaries. | standalone software, unix/linux, mac os x, windows, r, infrastructure, visualization, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:22937822 | Artistic License, v2 | biotools:ggbio, OMICS_04660 | http://www.tengfei.name/ggbio/ https://bio.tools/ggbio |
SCR_003313 | ggbio - Visualization tools for genomic data | 2025-04-19 06:41:39 | 13 | ||||||
|
NormFinder Resource Report Resource Website 1000+ mentions |
NormFinder (RRID:SCR_003387) | NormFinder | software resource | Software for identifying the optimal normalization gene among a set of candidates. It ranks the set of candidate normalization genes according to their expression stability in a given sample set and given experimental design. It can analyze expression data obtained through any quantitative method e.g. real time RT-PCR and microarray based expression analysis. NormFinder.xla adds the NormFinder functionality directly to Excel. A version for R is also available. | normalization, gene |
is used by: RefFinder is listed by: OMICtools |
PMID:15289330 | Free, Acknowledgement requested | OMICS_02317 | SCR_003387 | NormFinder software - Determine the optimal normalization gene | 2025-04-19 06:41:41 | 2302 | ||||||
|
deCODE genetics Resource Report Resource Website 10+ mentions |
deCODE genetics (RRID:SCR_003334) | deCODE | commercial organization | A biopharmaceutical company applying its discoveries in human genetics to develop drugs and diagnostics for common diseases. They specialize in gene discovery - their population approach and resources have enabled them to isolate key genes contributing to major public health challenges from cardiovascular disease to cancer. The company's genotyping capacity is now one of the highest in the world. They have a large population-based biobank containing whole blood and DNA samples with extensive relevant phenotypic information from around 120.000 Icelanders. In the company's work in more than 50 disease projects, their statistical and informatics departments have established themselves in data processing and analysis. deCODE genetics is widely recognized as a center of excellence in genetic research. | biopharmaceutical, genetics, drug, diagnostic, genotyping, phenotype, data processing, analysis, genetic variant, risk factor, genome, blood, dna, biobank, single nucleotide polymorphism |
is related to: EU-AIMS is related to: NEWMEDS |
Schizophrenia, Cardiovascular disease, Cancer, Type 2 diabetes, Atrial fibrillation, Heart attack | nif-0000-31959, ISNI: 0000 0004 0618 6889, grid.421812.c, Wikidata: Q493712 | https://ror.org/04dzdm737 | SCR_003334 | Islensk Erfdagreining EHF, Islensk Erfdagreining | 2025-04-19 06:41:40 | 48 | ||||||
|
PrimerSeq Resource Report Resource Website 1+ mentions |
PrimerSeq (RRID:SCR_003295) | PrimerSeq | software resource | Software that designs RT-PCR primers that evaluate alternative splicing events by incorporating RNA-Seq data. It is particularly advantageous for designing a large number of primers for validating alternative splicing events found in RNA-Seq data. It incorporates RNA-Seq data in the design process to weight exons by their read counts. Essentially, the RNA-Seq data allows primers to be placed using actually expressed transcripts. This could be for a particular cell line or experimental condition, rather than using annotations that incorporate transcripts that are not expressed for the data. Alternatively, you can design primers that are always on constitutive exons. PrimerSeq does not limit the use of gene annotations and can be used for a wide array of species. | primer, rna-seq, rt-pcr, windows, mac os x, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:24747190 | Apache License | biotools:primerseq, OMICS_02328 | https://bio.tools/primerseq | SCR_003295 | Primer Seek in RNA-Seq | 2025-04-19 06:41:39 | 7 | |||||
|
OmicCircos Resource Report Resource Website 50+ mentions |
OmicCircos (RRID:SCR_003292) | software resource | An R software application and package used to generate high-quality circular plots for visualizing genomic variations, including mutation patterns, copy number variations (CNVs), expression patterns, and methylation patterns. | standalone software, unix/linux, mac os x, windows, r, annotation, statistical method, visualization |
is listed by: OMICtools has parent organization: Bioconductor |
PMID:24526832 | GNU General Public License, v2 | OMICS_04659 | http://www.bioconductor.org/packages/release/bioc/html/OmicCircos.html | SCR_003292 | OmicCircos: High-quality circular visualization of omic data | 2025-04-19 06:41:39 | 73 | ||||||
|
MIPgen Resource Report Resource Website 10+ mentions |
MIPgen (RRID:SCR_003325) | software resource | Software for a fast, simple way to generate designs for MIP assays targeting hundreds or thousands of genomic loci in parallel. Packaged with MIPgen are scripts that aid in visualization of MIP designs and processing of MIP sequence reads to SAM files that can then be passed through any standard variant calling pipeline. | standalone software, c++, python, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: University of Washington; Seattle; USA |
PMID:24867941 | Non-commercial | OMICS_04657, biotools:mipgen | https://github.com/shendurelab/MIPGEN https://bio.tools/mipgen |
SCR_003325 | MIPgen - One stop MIP design and analysis | 2025-04-19 06:41:40 | 42 | ||||||
|
PoPoolation2 Resource Report Resource Website 100+ mentions |
PoPoolation2 (RRID:SCR_003284) | software resource | Software to compare allele frequencies for SNPs between two or more populations and to identify significant differences. PoPoolation2 requires next generation sequencing data of pooled genomic DNA (Pool-Seq). It may be used for measuring differentiation between populations, for genome wide association studies and for experimental evolution. | standalone software, next generation sequencing, population genetics, population genomics, statistics, toolkit, population |
is listed by: OMICtools has parent organization: Google Code |
PMID:22025480 | New BSD License | OMICS_05824 | SCR_003284 | 2025-04-19 06:41:39 | 230 | ||||||||
|
DAFGA Resource Report Resource Website 1+ mentions |
DAFGA (RRID:SCR_003319) | software resource | A python script package which estimates the evolutionary rate of a particular functional gene in a standardized manner by relating its sequence divergence to that of the 16S rRNA gene. It provides gene-specific parameter sets for OTU clustering and taxonomic assignment at desired rank, and it can be implemented into the diversity measurements offered by QIIME or Mothur. | standalone software, python | is listed by: OMICtools | PMID:24939150 | GNU General Public License, v3 or greater | OMICS_04654 | SCR_003319 | DAFGA: Diversity Analysis of Functional Gene Amplicons, Diversity analysis of Functional Gene Amplicons | 2025-04-19 06:41:40 | 1 | |||||||
|
Snakemake Resource Report Resource Website 100+ mentions |
Snakemake (RRID:SCR_003475) | Snakemake | software resource | A Python based language and execution environment for make-like workflows. The system supports the use of automatically inferred multiple named wildcards (or variables) in input and output filenames. | python, workflow, bio.tools |
is used by: RiboSnake is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:22908215 DOI:10.1093/bioinformatics/bts480 |
MIT License | OMICS_02299, biotools:snakemake | https://bio.tools/snakemake https://sources.debian.org/src/snakemake/ |
SCR_003475 | snakemake - A Python based language and execution environment for make-like workflows | 2025-04-19 06:41:44 | 286 | |||||
|
PheWAS R Package Resource Report Resource Website 1+ mentions |
PheWAS R Package (RRID:SCR_003512) | software resource | Software package contains methods for performing Phenome-Wide Association Study. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Vanderbilt University; Tennessee; USA |
PMID:20335276 | Free | OMICS_00242, biotools:phewas | https://bio.tools/phewas | SCR_003512 | Phenome-Wide Association Study | 2025-04-19 06:41:45 | 6 | ||||||
|
NGSANE Resource Report Resource Website 10+ mentions |
NGSANE (RRID:SCR_003478) | NGSANE | software resource | Software providing a Linux-based High Performance Computing (HPC) enabled framework for high-throughput data analysis that minimizes overhead for set up and processing of new projects yet maintains full flexibility of custom scripting when processing raw sequence data. | next generation sequencing | is listed by: OMICtools | PMID:24470576 | BSD License, v3 | OMICS_02298 | SCR_003478 | Next Generation Sequencing ANalysis for Enterprises | 2025-04-19 06:41:44 | 10 | ||||||
|
SNAPE-pooled Resource Report Resource Website 1+ mentions |
SNAPE-pooled (RRID:SCR_003476) | software resource | Software that computes the probability distribution for the frequency of the minor allele in a certain population, at a certain position in the genome. | standalone software |
is listed by: OMICtools has parent organization: Google Code |
PMID:22992255 | GNU General Public License, v3 | OMICS_05820 | SCR_003476 | snape-pooled: Computes the minor allele frequency spectrum in pooled DNA (sequenced) samples | 2025-04-19 06:41:44 | 7 | |||||||
|
Bpipe Resource Report Resource Website 10+ mentions |
Bpipe (RRID:SCR_003471) | Bpipe | software resource | Software tool for running and managing bioinformatics pipelines. It specializes in enabling users to turn existing pipelines based on shell scripts or command line tools into highly flexible, adaptable and maintainable workflows with a minimum of effort. Bpipe ensures that pipelines execute in a controlled and repeatable fashion and keeps audit trails and logs to ensure that experimental results are reproducible. Requiring only Java as a dependency, it is fully self-contained and cross-platform, making it very easy to adopt and deploy into existing environments. | genetics, dna, analysis, cluster, workflow, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Google Code |
PMID:22500002 | New BSD License, Acknowledgement requested | biotools:bpipe, OMICS_02301 | https://bio.tools/bpipe | SCR_003471 | bpipe - A tool for running and managing bioinformatics pipelines | 2025-04-19 06:41:44 | 13 | |||||
|
Parseq Resource Report Resource Website 1+ mentions |
Parseq (RRID:SCR_003464) | Parseq | software resource | Statistical software for transcription landscape reconstruction at a basepair resolution from RNA Seq read counts. It is based on a state-space model which describes, in terms of abrupt shifts and more progressive drifts, the transcription level dynamics along the genome. Alongside variations of transcription level, it incorporates a component of short-range variation to pull apart local artifacts causing correlated dispersion. Reconstruction of the transcription level relies on a conditional sequential Monte Carlo approach that is combined with parameter estimation in a Markov chain Monte Carlo algorithm known as particle Gibbs. The method allows to estimate the local transcription level, to call transcribed regions, and to identify the transcript borders. | rna-seq, genome, transcription, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Sorbonne University; Paris; France |
PMID:24470570 | biotools:parseq, OMICS_02302 | https://bio.tools/parseq | SCR_003464 | 2025-04-19 06:41:44 | 2 | |||||||
|
GBSA Resource Report Resource Website 1+ mentions |
GBSA (RRID:SCR_003413) | GBSA | software resource | Software for analyzing whole-genome bisulfite sequencing data. |
is listed by: OMICtools has parent organization: National University of Singapore; Singapore; Singapore |
PMID:23268441 | GNU General Public License, v3, Acknowledgement requested | OMICS_00600 | SCR_003413 | Genome-Wide Bisulfite Sequencing Analyser Software, GBSA - Genome-Wide Bisulfite Sequencing Analyser Software | 2025-04-19 06:41:42 | 2 | |||||||
|
MultiPhen Resource Report Resource Website 10+ mentions |
MultiPhen (RRID:SCR_003498) | software resource | Software package that performs genetic association tests between SNPs (one-at-a-time) and multiple phenotypes (separately or in joint model). | standalone software, r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: CRAN |
PMID:22567092 | GNU General Public License, v2 | biotools:multiphen, OMICS_04397 | https://bio.tools/multiphen | SCR_003498 | MultiPhen: a package for the genetic association testing of multiple phenotypes | 2025-04-19 06:41:45 | 27 |
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