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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
|
oneChannelGUI Resource Report Resource Website 10+ mentions |
oneChannelGUI (RRID:SCR_001325) | oneChannelGUI | software resource | Software library that provides a graphical interface for microarray gene and exon level analysis as well as miRNA/mRNA-seq data analysis. The package was developed to simplify the use of Bioconductor tools for beginners having limited or no experience in writing R code. | differential expression, gui, microarray, multiple comparison, preprocessing, quality control, rna-seq, exon, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:17875544 | Free, Available for download, Freely available | biotools:onechannelgu, OMICS_02004 | http://www.bioconductor.org/packages/release/bioc/html/oneChannelGUI.html | SCR_001325 | 2026-02-14 02:00:01 | 13 | ||||||
|
CYCLE Resource Report Resource Website 10+ mentions |
CYCLE (RRID:SCR_001328) | CYCLE | software resource | Software package for the identification of periodically expressed genes using Fourier analysis and the statistical assessment of significance using different background models. | r, microarray, time course, periodic expression pattern, time-series, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Humboldt University of Berlin; Berlin; Germany has parent organization: Bioconductor |
PMID:18310054 | THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_02010, biotools:cycle | http://www.bioconductor.org/packages/release/bioc/html/cycle.html https://bio.tools/cycle |
SCR_001328 | 2026-02-14 02:00:06 | 31 | ||||||
|
affylmGUI Resource Report Resource Website 10+ mentions |
affylmGUI (RRID:SCR_001320) | affylmGUI | software resource | R software package providing a Graphical User Interface for analysis of Affymetrix microarray data, using the limma package (Linear Models for MicroArray data). While not as powerful as limma to the expert user, it offers a simple point-and-click interface to many of the commonly-used limma and affy functions. You need to have R 1.9.0 or later, Tcl/Tk 8.3 or later (ActiveTcl for Windows, Tcl/Tk Source for Linux/Unix, or X11 Tcl/Tk for MacOSX) and the limma, affylmGUI, and tkrplot R packages. It has been succesfully tested on Windows 2000, Windows XP, RedHat/Fedora Linux, and on Mac OSX with X11. | affymetrix, differential expression, r, data import, differential expression, gui, microarray, multiple comparison, one channel, preprocessing, quality control, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Walter and Eliza Hall Institute of Medical Research; Victoria; Australia has parent organization: Bioconductor |
PMID:16455752 | Free, Available for download, Freely available | biotools:affylmgui, OMICS_02016 | http://www.bioconductor.org/packages/release/bioc/html/affylmGUI.html https://bio.tools/affylmgui |
SCR_001320 | Affymetrix linear modeling Graphical User Interface | 2026-02-14 02:00:06 | 31 | |||||
|
plgem Resource Report Resource Website 10+ mentions |
plgem (RRID:SCR_001355) | plgem | software resource | Software to detect differential expression in microarray and proteomics datasets. Its use has been shown to improve the detection of differentially expressed genes or proteins in these datasets. | differential expression, microarray, proteomics, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_01984, biotools:plgem | https://bio.tools/plgem | SCR_001355 | Power Law Global Error Model | 2026-02-14 02:00:01 | 16 | ||||||
|
fRMA Resource Report Resource Website 50+ mentions |
fRMA (RRID:SCR_001345) | fRMA | software resource | Preprocessing and analysis software for single microarrays and microarray batches. | microarray, preprocessing, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:23044545 | Free, Available for download, Freely available | biotools:frma, OMICS_01994 | https://bio.tools/frma | SCR_001345 | fRMA - Frozen RMA and Barcode | 2026-02-14 02:00:01 | 74 | |||||
|
dyebias Resource Report Resource Website |
dyebias (RRID:SCR_001308) | dyebias | software resource | Software package using the GASSCO method for correcting for slide-dependent gene-specific dye bias. | microarray, preprocessing, quality control, two channel, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
PMID:17623705 | GNU General Public License, v3 | biotools:dyebias, OMICS_02025 | https://bio.tools/dyebias | SCR_001308 | dyebias - The GASSCO method for correcting for slide-dependent gene-specific dye bias | 2026-02-14 01:59:58 | 0 | |||||
|
limmaGUI Resource Report Resource Website 10+ mentions |
limmaGUI (RRID:SCR_001306) | limmaGUI | software resource | Software package for a Graphical User Interface for the limma Microarray package. | differential expression, gui, microarray, multiple comparison, preprocessing, quality control, two channel, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: Bioconductor |
PMID:15297296 | Free, Available for download, Freely available | OMICS_02027, biotools:limmagui | https://bio.tools/limmagui | SCR_001306 | limmaGUI - GUI for limma package | 2026-02-14 02:00:05 | 14 | |||||
|
ffpe Resource Report Resource Website 100+ mentions |
ffpe (RRID:SCR_001307) | ffpe | software resource | Software to identify low-quality data using metrics developed for expression data derived from Formalin-Fixed, Paraffin-Embedded (FFPE) data. Also a function for making Concordance at the Top plots (CAT-plots). | formalin-fixed, paraffin-embedded, gene expression, microarray, quality control, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: Bioconductor |
Free, Available for download, Freely available | OMICS_02026, biotools:ffpe | https://bio.tools/ffpe | SCR_001307 | ffpe - Quality assessment and control for FFPE microarray expression data | 2026-02-14 02:00:00 | 496 | ||||||
|
Eddy Lab Software Resource Report Resource Website 10+ mentions |
Eddy Lab Software (RRID:SCR_001458) | software resource | Software library containing tools for statistical manipulations of data. Tools include profile hidden Markov models for biological sequence analysis, RNA structure analysis, and a prototype noncoding RNA genefinder. | software repository, statistics, data, statistical analysis, statistical manipulation, markov model, bio.tools |
is listed by: bio.tools is listed by: Debian has parent organization: Janelia Research has parent organization: Howard Hughes Medical Institute |
Free, Available for download, Freely available | nif-0000-08778, biotools:pknots | https://bio.tools/pknots | http://selab.janelia.org/software.html | SCR_001458 | Eddy Lab: Software, Eddy Lab - Software | 2026-02-14 02:00:04 | 21 | ||||||
|
PyLOH Resource Report Resource Website 1+ mentions |
PyLOH (RRID:SCR_001511) | software resource | Software for deconvolving tumor purity and ploidy by integrating copy number alterations and loss of heterozygosity. The model resolves the identifiability problem by integrating two types of sequencing information - somatic copy number alterations and loss of heterozygosity - within an unified probabilistic framework. | standalone software, python, bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
PMID:24695406 | Free, Available for download, Freely available | OMICS_03559, biotools:pyloh | https://bio.tools/pyloh | SCR_001511 | 2026-02-14 02:00:04 | 4 | |||||||
|
EpiGRAPH Resource Report Resource Website 10+ mentions |
EpiGRAPH (RRID:SCR_004326) | EpiGRAPH | software resource | A software for genome and epigenome analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian |
THIS RESOURCE IS NO LONGER IN SERVICE | OMICS_00633, biotools:epigraph | https://bio.tools/epigraph | SCR_004326 | 2026-02-14 02:00:39 | 18 | |||||||
|
InsertionMapper Resource Report Resource Website |
InsertionMapper (RRID:SCR_004163) | InsertionMapper | software resource | A pipeline tool for the identification of targeted sequences from multidimensional high throughput sequencing data. It consists of four independently working modules: Data Preprocessing, Database Modeling, Dimension Deconvolution and Element Mapping. This pipeline tool is applicable to scenarios requiring analysis of the tremendous output of short reads produced in NGS sequencing experiments of targeted genome sequences. | high throughput sequencing, dna sequence, next generation sequencing, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: SourceForge has parent organization: Montclair State University; New Jersey; USA |
PMID:24090499 | Acknowledgement requested, GNU General Public License | OMICS_01547, biotools:insertionmapper | https://bio.tools/insertionmapper | SCR_004163 | 2026-02-14 02:00:37 | 0 | ||||||
|
bcbio-nextgen Resource Report Resource Website 100+ mentions |
bcbio-nextgen (RRID:SCR_004316) | bcbio-nextgen | software resource | A python toolkit providing best-practice pipelines for fully automated high throughput sequencing analysis. | mapreduce/hadoop, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
Free, Available for download, Freely available | biotools:bcbio-nextgen, OMICS_01121, BioTools:bcbio-nextgen | https://github.com/chapmanb/bcbb/blob/master/nextgen/README.md https://bio.tools/bcbio-nextgen https://bio.tools/bcbio-nextgen |
SCR_004316 | 2026-02-14 02:00:39 | 155 | |||||||
|
TagDust Resource Report Resource Website 50+ mentions |
TagDust (RRID:SCR_004175) | TagDust | software resource | A program to eliminate artifactual reads from next-generation sequencing data sets. | unix/linux, bio.tools, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:19737799 | biotools:tagdust, OMICS_01095, biotools:nexalign | https://bio.tools/tagdust https://bio.tools/nexalign |
SCR_004175 | 2026-02-14 02:00:37 | 54 | |||||||
|
Artemis: Genome Browser and Annotation Tool Resource Report Resource Website 100+ mentions |
Artemis: Genome Browser and Annotation Tool (RRID:SCR_004267) | Artemis | software resource | THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Free genome browser and annotation tool that allows visualization of sequence features, next generation data and the results of analyses within the context of the sequence, and also its six-frame translation. Artemis is free software and is distributed under the terms of the GNU General Public License. Artemis is written in Java, and is available for UNIX, Macintosh and Windows systems. It can read EMBL and GENBANK database entries or sequence in FASTA, indexed FASTA or raw format. Other sequence features can be in EMBL, GENBANK or GFF format. | training tool, genome browser, gene annotation, java, bio.tools |
is listed by: OMICtools is listed by: 3DVC is listed by: Debian is listed by: bio.tools is related to: DNAPlotter has parent organization: Wellcome Trust Sanger Institute; Hinxton; United Kingdom works with: Alien-hunter |
Wellcome Trust | PMID:11120685 DOI:10.1093/bioinformatics/btr703 |
THIS RESOURCE IS NO LONGER IN SERVICE | nlx_28554, OMICS_00903, biotools:artemis | https://bio.tools/artemis https://sources.debian.org/src/art-nextgen-simulation-tools/ |
SCR_004267 | 2026-02-14 02:00:56 | 421 | |||||
|
SnoopCGH Resource Report Resource Website 1+ mentions |
SnoopCGH (RRID:SCR_004420) | SnoopCGH | software resource | A java desktop application for visualising and exploring comparative genomic hybridization (CGH) data. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: SourceForge |
PMID:19687029 | biotools:snoopcgh, OMICS_00736 | https://bio.tools/snoopcgh | SCR_004420 | 2026-02-14 02:00:40 | 2 | |||||||
|
GASSST Resource Report Resource Website 1+ mentions |
GASSST (RRID:SCR_004413) | GASSST | software resource | Software that finds global alignments of short DNA sequences against large DNA banks. It is able to perform fast gapped alignments and works well for both short and longer reads. It has been tested for reads up to 500bp. | bio.tools |
is listed by: OMICtools is listed by: bio.tools is listed by: Debian has parent organization: University of Rennes 1; Rennes; France |
PMID:20739310 | CeCILL license, v2 | biotools:gassst, OMICS_00663 | https://bio.tools/gassst | SCR_004413 | GASSST : Global Alignment Short Sequence Search Tool, Global Alignment Short Sequence Search Tool | 2026-02-14 02:00:40 | 7 | |||||
|
Distributed String Mining Framework Resource Report Resource Website 1+ mentions |
Distributed String Mining Framework (RRID:SCR_004736) | dsm-framework | software resource | Software package providing distributed string mining for High-Throughput Sequencing data that provides a content-based exploration and retrieval method for whole metagenome sequencing samples. | gpu/cuda, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools |
PMID:24845653 | GNU General Public License, v2 or greater | biotools:dsm, OMICS_04171 | https://bio.tools/dsm | SCR_004736 | 2026-02-14 02:01:00 | 1 | ||||||
|
DELLY Resource Report Resource Website 500+ mentions |
DELLY (RRID:SCR_004603) | DELLY | software resource | Integrated structural variant prediction software that can detect deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. It uses paired-ends and split-reads to sensitively and accurately delineate genomic rearrangements throughout genome. | structural variant, genomic rearrangement, deletion, tandem duplication, inversion, translocation, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: European Molecular Biology Laboratory |
PMID:22962449 DOI:10.1093/bioinformatics/bts378 |
OMICS_00313, biotools:delly2 | https://bio.tools/delly2 https://github.com/dellytools/delly/ https://sources.debian.org/src/delly/ |
SCR_004603 | DELLY, Structural variant discovery by integrated paired-end and split-read analysis | 2026-02-14 02:00:59 | 557 | ||||||
|
Kdetrees Resource Report Resource Website |
Kdetrees (RRID:SCR_004522) | software resource | R package using a non-parametric method for estimating distributions of phylogenetic trees, with the goal of identifying trees that are significantly different from the rest of the trees in the sample. | applet, mac os x, unix/linux, windows, r, bio.tools |
is listed by: OMICtools is listed by: Debian is listed by: bio.tools has parent organization: CRAN |
PMID:24764459 | GNU General Public License, v2 | biotools:kdetrees, OMICS_04172 | https://github.com/grady/kdetrees https://bio.tools/kdetrees |
SCR_004522 | kdetrees: Nonparametric method for identifying discordant phylogenetic trees | 2026-02-14 02:00:58 | 0 |
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