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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
SNVMix Resource Report Resource Website 1+ mentions |
SNVMix (RRID:SCR_013050) | SNVMix | software resource | Software designed to detect single nucleotide variants from next generation sequencing data. |
is listed by: OMICtools has parent organization: University of British Columbia; British Columbia; Canada |
OMICS_00077 | SCR_013050 | 2026-08-01 12:04:44 | 1 | ||||||||||
|
TurboNorm Resource Report Resource Website |
TurboNorm (RRID:SCR_012963) | TurboNorm | software resource | Software providing a fast scatterplot smoother suitable for microarray normalization based on B-splines with second-order difference penalty. Functions for microarray normalization of single-colour data i.e. Affymetrix/Illumina and two-colour data supplied as marray MarrayRaw-objects or limma RGList-objects are available. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00856 | SCR_012963 | 2026-08-01 12:04:42 | 0 | ||||||||||
|
ProbeSelect Resource Report Resource Website 1+ mentions |
ProbeSelect (RRID:SCR_012965) | ProbeSelect | software resource | Software for selecting probes in heterogenous transcriptional sets. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00836 | SCR_012965 | ProbeSelect - Selecting probes in heterogenous transcriptional sets | 2026-08-01 12:04:43 | 4 | |||||||||
|
SeqGenome Browser Resource Report Resource Website |
SeqGenome Browser (RRID:SCR_012970) | SeqGenome Browser | software resource | Mini cross-platform local genome browser software designed for visualizing next-generation sequencing data. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
GNU General Public License, v2 | OMICS_00924 | SCR_012970 | 2026-08-01 12:04:54 | 0 | ||||||||
|
GBrowse syn Resource Report Resource Website 1+ mentions |
GBrowse syn (RRID:SCR_012971) | GBrowse_syn | software resource | A GBrowse-based synteny browser designed to display multiple genomes, with a central reference species compared to two or more additional species. |
is listed by: OMICtools has parent organization: Generic Model Organism Database Project |
OMICS_00935 | SCR_012971 | Generic Synteny Browser | 2026-08-01 12:04:43 | 9 | |||||||||
|
miRDeep-P Resource Report Resource Website 1+ mentions |
miRDeep-P (RRID:SCR_013026) | miRDP | software resource | A computational tool for analyzing the microRNA (miRNA) transcriptome in plants. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:21775303 | GNU General Public License, v3 | OMICS_00375 | SCR_013026 | 2026-08-01 12:04:54 | 6 | ||||||||
|
Ringo Resource Report Resource Website 10+ mentions |
Ringo (RRID:SCR_012973) | Ringo | software resource | Software package that facilitates the primary analysis of ChIP-chip data. |
is listed by: OMICtools is listed by: SoftCite has parent organization: Bioconductor |
OMICS_00809 | SCR_012973 | 2026-08-01 12:04:54 | 38 | ||||||||||
|
CRAM Resource Report Resource Website 500+ mentions |
CRAM (RRID:SCR_012975) | CRAM | software resource | A framework technology comprising file format and toolkit in which we combine highly efficient and tunable reference-based compression of sequence data with a data format that is directly available for computational use. |
is listed by: OMICtools has parent organization: European Bioinformatics Institute |
PMID:21245279 | OMICS_00952 | SCR_012975 | 2026-08-01 12:04:42 | 722 | |||||||||
|
KungFq Resource Report Resource Website |
KungFq (RRID:SCR_012979) | KungFq | software resource | Tool that compresses and decompresses fastq files. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23221092 | OMICS_00962 | SCR_012979 | 2026-08-01 12:04:42 | 0 | |||||||||
|
ncPRO-seq Resource Report Resource Website 1+ mentions |
ncPRO-seq (RRID:SCR_013031) | ncPRO-seq | software resource | Software that aims to interrogate and perform detailed analysis on small RNAs derived from annotated non-coding regions. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23044543 | OMICS_00366 | SCR_013031 | ncPRO-seq - A tool for annotation and profiling of ncRNAs from small RNA sequencing data | 2026-08-01 12:04:44 | 9 | ||||||||
|
vcf2MSAT Resource Report Resource Website |
vcf2MSAT (RRID:SCR_013034) | vcf2MSAT | software resource | A python software program to identify microsatellite repeat regions based on known polymorphisms identified in a .vcf report after using SAMtools to analyze next-generation sequencing files. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_00118 | SCR_013034 | vcf2MSAT - Find Microsatellites in a .vcf report | 2026-08-01 12:04:54 | 0 | |||||||||
|
FishingCNV Resource Report Resource Website 10+ mentions |
FishingCNV (RRID:SCR_013038) | FishingCNV | software resource | A software tool developed at McGill University, is a tool for comprehensive analysis of rare copy number variations in high-throughput exome sequencing data. |
is listed by: OMICtools has parent organization: SourceForge |
PMID:23539306 | Commercial license | OMICS_00334 | SCR_013038 | FishingCNV - Copy number variation detection in exome sequencing data, FishingCNV - CNV detection in exome sequencing data, FishingCNV - Copy number variation (CNV) detection in exome sequencing data | 2026-08-01 12:04:55 | 11 | |||||||
|
MSAProbs Resource Report Resource Website 10+ mentions |
MSAProbs (RRID:SCR_012982) | MSAProbs | software resource | An open-source protein multiple sequence ailgnment algorithm, achieving the stastistically highest alignment accuracy on popular benchmarks. | c++ |
is listed by: OMICtools has parent organization: SourceForge |
PMID:20576627 | GNU General Public License, v3 | OMICS_00980 | SCR_012982 | MSAProbs: Multiple Sequence Alignment | 2026-08-01 12:04:54 | 19 | ||||||
|
QcReads Resource Report Resource Website 1+ mentions |
QcReads (RRID:SCR_013002) | QcReads | software resource | Provides an efficient tool for trimming adapter sequences and low quality sequences, in raw reads generated by the high throughput sequencing platforms. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01088 | SCR_013002 | 2026-08-01 12:04:54 | 1 | ||||||||||
|
SeqPrep Resource Report Resource Website 500+ mentions |
SeqPrep (RRID:SCR_013004) | SeqPrep | software resource | A program to merge paired end Illumina reads that are overlapping into a single longer read. | bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
biotools:seqprep, OMICS_01092 | https://bio.tools/seqprep, https://sources.debian.org/src/seqprep/ | SCR_013004 | SeqPrep - Tool for stripping adaptors and/or merging paired reads with overlap into single reads | 2026-08-01 12:04:43 | 977 | |||||||
|
phyloseq Resource Report Resource Website 1000+ mentions |
phyloseq (RRID:SCR_013080) | phyloseq | software resource | Software for handling and analysis of high-throughput microbiome census data. | bio.tools |
is used by: microViz is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
DOI:10.1371/journal.pone.0061217 | OMICS_01520, biotools:phyloseq | https://bio.tools/phyloseq, https://sources.debian.org/src/r-bioc-phyloseq/ | SCR_013080 | 2026-08-01 12:04:45 | 2774 | |||||||
|
PhyloPhlAn Resource Report Resource Website 100+ mentions |
PhyloPhlAn (RRID:SCR_013082) | PhyloPhlAn | software resource | Software pipeline for reconstructing highly accurate and resolved phylogenetic trees based on whole-genome sequence information. Pipeline is scalable to thousands of genomes and uses the most conserved 400 proteins for extracting the phylogenetic signal. PhyloPhlAn also implements taxonomic curation, estimation, and insertion operations., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | phylogenetic tree, whole-genome sequence, genome, protein |
is listed by: OMICtools is listed by: Debian has parent organization: Harvard T.H. Chan School of Public Health |
PMID:23942190 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_01525 | https://sources.debian.org/src/phylophlan/ | SCR_013082 | PhyloPhlAn: microbial Tree of Life using 400 universal proteins | 2026-08-01 12:04:55 | 339 | |||||
|
HECTOR Resource Report Resource Website 50+ mentions |
HECTOR (RRID:SCR_013007) | HECTOR | software resource | A parallel multistage k-hopo spectrum based homopolymer-length error corrector for 454 sequencing data. |
is listed by: OMICtools has parent organization: SourceForge |
OMICS_01104 | SCR_013007 | HECTOR: Parallel error corrector for 454 datasets | 2026-08-01 12:04:44 | 55 | |||||||||
|
BayesPeak Resource Report Resource Website 10+ mentions |
BayesPeak (RRID:SCR_013011) | BayesPeak | software resource | Software package that is an implementation of the BayesPeak algorithm for peak-calling in ChIP-seq data. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00432 | SCR_013011 | BayesPeak - Bayesian Analysis of ChIP-seq Data | 2026-08-01 12:04:44 | 13 | |||||||||
|
ChIPseqR Resource Report Resource Website |
ChIPseqR (RRID:SCR_013016) | ChIPseqR | software resource | Software that identifies protein binding sites from ChIP-seq and nucleosome positioning experiments. |
is listed by: OMICtools has parent organization: Bioconductor |
OMICS_00501 | SCR_013016 | 2026-08-01 12:04:44 | 0 |
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