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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
TETRA Resource Report Resource Website 50+ mentions |
TETRA (RRID:SCR_004573) | TETRA | software resource | Standalone software programs that can be used to calculate how well tetranucleotide usage patterns in DNA sequences correlate. Such correlations can provide valuable hints on the relatedness of DNA sequences. | tetranucleotide, dna sequence |
is listed by: OMICtools has parent organization: Max Planck Institute for Marine Microbiology; Bremen; Germany |
PMID:15305919 PMID:15507136 |
OMICS_01474 | SCR_004573 | TETRA - Fragment assignment by intrinsic tetranucleotide frequencies | 2026-02-07 02:06:49 | 66 | |||||||
|
BioPig Resource Report Resource Website 1+ mentions |
BioPig (RRID:SCR_004636) | BioPig | software resource | Software providing a framework for genomic data analysis using Apache Pig and Hadoop. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Lawrence Berkeley National Laboratory |
PMID:24021384 | biotools:biopig, OMICS_01225 | https://bio.tools/biopig | SCR_004636 | 2026-02-07 02:06:25 | 2 | |||||||
|
Nonpareil Resource Report Resource Website 50+ mentions |
Nonpareil (RRID:SCR_004629) | Nonpareil | software resource | Estimate average coverage and create Nonpareil curves for metagenomic datasets. | is listed by: OMICtools | PMID:24123672 | OMICS_01419 | SCR_004629 | 2026-02-07 02:06:50 | 78 | |||||||||
|
AbundanceBin Resource Report Resource Website 1+ mentions |
AbundanceBin (RRID:SCR_004648) | AbundanceBin | software resource | An abundance-based software tool for binning metagenomic sequences, such that the reads classified in a bin belong to species of identical or very similar abundances. AbundanceBin also gives estimations of species abundances and their genome sizes -two important characteristic parameters for a microbial community. | metagenome, sequence |
is listed by: OMICtools has parent organization: Indiana University; Indiana; USA |
PMID:21385052 | Acknowledgement requested, Free, Public | OMICS_01471 | SCR_004648 | 2026-02-07 02:06:25 | 6 | |||||||
|
VariationHunter Resource Report Resource Website 10+ mentions |
VariationHunter (RRID:SCR_004865) | VariationHunter | software resource | A software tool for discovery of structural variation in one or more individuals simultaneously using high throughput technologies. | structural variation, genome, next-generation sequencing |
is listed by: OMICtools is related to: SPLITREAD has parent organization: Simon Fraser University; British Columbia; Canada has parent organization: SourceForge |
PMID:22048523 PMID:20529927 |
OMICS_00328 | SCR_004865 | VariationHunter-CommonLaw | 2026-02-07 02:06:33 | 12 | |||||||
|
Phymm and PhymmBL Resource Report Resource Website 10+ mentions |
Phymm and PhymmBL (RRID:SCR_004751) | Phymm, PhymmBL | software resource | Software for Phylogenetic Classification of Metagenomic Data with Interpolated Markov Models to taxonomically classify DNA sequences and accurately classify reads as short as 100 bp. PhymmBL, the hybrid classifier included in this distribution which combines analysis from both Phymm and BLAST, produces even higher accuracy. | metagenome, sequence, taxonomy, classification, phylogenetic classification, genome, short read |
is listed by: OMICtools has parent organization: University of Maryland; Maryland; USA |
NLM R01-LM006845 | PMID:19648916 PMID:21527926 |
Open-source license | OMICS_01461 | SCR_004751 | 2026-02-07 02:06:53 | 12 | ||||||
|
deStruct Resource Report Resource Website 1+ mentions |
deStruct (RRID:SCR_004747) | deStruct | software resource | A software tool for identifying structural variation in tumour genomes from whole genome illumina sequencing. | structural variation, genome, genomics |
is listed by: OMICtools has parent organization: Google Code |
Tumor, Cancer | Open unspecified license | OMICS_00314 | SCR_004747 | deStruct - Bioinformatics tool for identifying structural variation in tumour genomes | 2026-02-07 02:06:53 | 7 | ||||||
|
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 | Free, Available for download, Freely available | biotools:aldex2, OMICS_04634 | https://bio.tools/aldex2 | SCR_003364 | 2026-02-07 02:06:00 | 492 | |||||||
|
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 | Free, Available for download, Freely available | OMICS_04661 | https://bitbucket.org/henryhzhang/rcircos/ | SCR_003310 | RCircos: Circos 2D Track Plot | 2026-02-07 02:06:16 | 229 | ||||||
|
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 | Free, Available for download, Freely available | OMICS_02330 | SCR_003275 | 2026-02-07 02:05:59 | 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 |
Free, Available for download, Freely available | OMICS_02312 | SCR_003396 | Delta-Delta-Ct | 2026-02-07 02:06:02 | 319 | |||||||
|
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 | Free, Available for download, Freely available | biotools:ggbio, OMICS_04660 | http://www.tengfei.name/ggbio/ https://bio.tools/ggbio |
SCR_003313 | ggbio - Visualization tools for genomic data | 2026-02-07 02:06:16 | 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, Available for download, Freely available | OMICS_02317 | https://www.moma.dk/software/normfinder | SCR_003387 | NormFinder software - Determine the optimal normalization gene | 2026-02-07 02:06:02 | 2382 | |||||
|
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 | Free, Available for download, Freely available | biotools:primerseq, OMICS_02328 | https://bio.tools/primerseq | SCR_003295 | Primer Seek in RNA-Seq | 2026-02-07 02:06:15 | 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 | Free, Available for download, Freely available | OMICS_04659 | http://www.bioconductor.org/packages/release/bioc/html/OmicCircos.html | SCR_003292 | OmicCircos: High-quality circular visualization of omic data | 2026-02-07 02:05:59 | 78 | ||||||
|
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 | Free, Available for download, Freely available | OMICS_04657, biotools:mipgen | https://github.com/shendurelab/MIPGEN https://bio.tools/mipgen |
SCR_003325 | MIPgen - One stop MIP design and analysis | 2026-02-07 02:06:00 | 47 | ||||||
|
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., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | standalone software, next generation sequencing, population genetics, population genomics, statistics, toolkit, population |
is listed by: OMICtools has parent organization: Google Code |
PMID:22025480 | Free, Available for download, Freely available | OMICS_05824 | SCR_003284 | 2026-02-07 02:06:15 | 242 | ||||||||
|
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 | Free, Available for download, Freely available | OMICS_04654 | SCR_003319 | DAFGA: Diversity Analysis of Functional Gene Amplicons, Diversity analysis of Functional Gene Amplicons | 2026-02-07 02:06:16 | 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 |
Free, Available for download, Freely available | OMICS_02299, biotools:snakemake | https://snakemake.github.io/ | SCR_003475 | snakemake - A Python based language and execution environment for make-like workflows | 2026-02-07 02:06:20 | 353 | |||||
|
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 | 2026-02-07 02:06:21 | 6 |
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