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http://www.broadinstitute.org/gsea/
Software package for interpreting gene expression data. Used for interpretation of a large-scale experiment by identifying pathways and processes.
Proper citation: Gene Set Enrichment Analysis (RRID:SCR_003199) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 27,2023. A simple tab-delimited, spreadsheet-based format which will become a part of the MAGE microarray data standard that can be used for annotating and communicating microarray data in a MIAME compliant fashion. MAGE-TAB will enable laboratories without bioinformatics experience or support to manage, exchange and submit well-annotated microarray data in a standard format using a spreadsheet. The MAGE-TAB format is self-contained, and does not require an understanding of MAGE-ML or XML.
Proper citation: MAGE-TAB (RRID:SCR_003222) Copy
http://creskolab.uoregon.edu/stacks/
A software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. It was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography.
Proper citation: Stacks (RRID:SCR_003184) Copy
http://bibiserv.techfak.uni-bielefeld.de/rnahybrid/
Software tool for finding the minimum free energy hybridization of a long and a short RNA. The hybridization is performed in a kind of domain mode, i.e., the short sequence is hybridized to the best fitting part of the long one. The tool is primarily meant as a means for microRNA target prediction.
Proper citation: RNAhybrid (RRID:SCR_003252) Copy
https://github.com/mozack/abra
Software that is a realigner for next generation sequencing data. It uses localized assembly and global realignment to align reads more accurately, thus improving downstream analysis (detection of indels and complex variants in particular).
Proper citation: Assembly Based ReAligner (RRID:SCR_003277) Copy
Central online repository for microRNA nomenclature, sequence data, annotation and target prediction.Collection of published miRNA sequences and annotation.
Proper citation: miRBase (RRID:SCR_003152) Copy
http://www.bioconductor.org/packages/release/bioc/html/QDNAseq.html
Software package for quantitative DNA sequencing for chromosomal aberrations providing a robust, cost-effective WGS method for DNA copy number analysis. The genome is divided into non-overlapping fixed-sized bins, number of sequence reads in each counted, adjusted with a simultaneous two-dimensional loess correction for sequence mappability and GC content, and filtered to remove spurious regions in the genome. Downstream steps of segmentation and calling are also implemented via packages DNAcopy and CGHcall, respectively.
Proper citation: QDNAseq (RRID:SCR_003174) Copy
A free, open-source, computationally efficient Java program for comparative analyses of QTL mapping data and population simulation that runs on any computer operating system. (entry from Genetic Analysis Software) It is written with a plug-in architecture for ready extensibility. The software accommodates line-cross mating designs consisting of any arbitrary sequence of selfing, backcrossing, intercrossing and haploid-doubling steps that includes map, population, and trait simulators; and is scriptable. Source code is available on request.
Proper citation: QGene (RRID:SCR_003209) Copy
http://compgen.bscb.cornell.edu/phast/
A freely available software package for comparative and evolutionary genomics that consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations. For the most part, PHAST focuses on two kinds of applications: the identification of novel functional elements, including protein-coding exons and evolutionarily conserved sequences; and statistical phylogenetic modeling, including estimation of model parameters, detection of signatures of selection, and reconstruction of ancestral sequences. It consists of over 60,000 lines of C code.
Proper citation: PHAST (RRID:SCR_003204) Copy
https://github.com/hangelwen/miR-PREFeR
An accurate, fast, and easy-to-use plant miRNA prediction software tool using small RNA-Seq data. It utilizes expression patterns of miRNA and follows the criteria for plant microRNA annotation to accurately predict plant miRNAs from one or more small RNA-Seq data samples of the same species.
Proper citation: miR-PREFeR (RRID:SCR_003353) Copy
An algorithm for the identification of microRNA targets. Details are provided (3' UTR alignments with predicted sites, links to various public databases etc) regarding: # microRNA target predictions in vertebrates (Krek et al, Nature Genetics 37:495-500 (2005)) # microRNA target predictions in seven Drosophila species (Grn et al, PLoS Comp. Biol. 1:e13 (2005)) # microRNA targets in three nematode species (Lall et al, Current Biology 16, 1-12 (2006)) # human microRNA targets that are not conserved but co-expressed (i.e. the microRNA and mRNA are expressed in the same tissue) (Chen and Rajewsky, Nat Genet 38, 1452-1456 (2006)) co-expressed targets
Proper citation: PicTar (RRID:SCR_003343) Copy
https://planttfdb.gao-lab.org/
Comprehensive plant transcription factor database. Interface to allow users to search the database by IDs or free texts, to make sequence similarity search against TFs of all or individual species, and to download TF sequences for local analysis.PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors
Proper citation: PLANTTFDB (RRID:SCR_003362) Copy
http://www.genetics.ucla.edu/labs/horvath/CoexpressionNetwork/
Software R package for weighted correlation network analysis. WGCNA is also available as point-and-click application. Unfortunately this application is not maintained anymore. It is known to have compatibility problems with R-2.8.x and newer, and the methods it implements are not all state of the art., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Weighted Gene Co-expression Network Analysis (RRID:SCR_003302) Copy
http://www.bioconductor.org/packages/release/bioc/html/NormqPCR.html
Software package providing functions for the selection of optimal reference genes and the normalization of real-time quantitative PCR data.
Proper citation: NormqPCR (RRID:SCR_003388) Copy
Data collection for Xenopus laevis and Xenopus tropicalis biology and genomics.
Proper citation: Xenbase (RRID:SCR_003280) Copy
http://discovery.hsci.harvard.edu/
An online database of curated cancer stem cell (CSC) experiments coupled to the Galaxy analytical framework. Driven by a need to improve our understanding of molecular processes that are common and unique across cancer stem cells (CSCs), the SCDE allows users to consistently describe, share and compare CSC data at the gene and pathway level. The initial focus has been on carefully curating tissue and cancer stem cell-related experiments from blood, intestine and brain to create a high quality resource containing 53 public studies and 1098 assays. The experimental information is captured and stored in the multi-omics Investigation/Study/Assay (ISA-Tab) format and can be queried in the data repository. A linked Galaxy framework provides a comprehensive, flexible environment populated with novel tools for gene list comparisons against molecular signatures in GeneSigDB and MSigDB, curated experiments in the SCDE and pathways in WikiPathways. Investigation/Study/Assay (ISA) infrastructure is the first general-purpose format and freely available desktop software suite targeted to experimentalists, curators and developers and that: * assists in the reporting and local management of experimental metadata (i.e. sample characteristics, technology and measurement types, sample-to-data relationships) from studies employing one or a combination of technologies; * empowers users to uptake community-defined minimum information checklists and ontologies, where required; * formats studies for submission to a growing number of international public repositories endorsing the tools, currently ENA (genomics), PRIDE (proteomics) and ArrayExpress (transcriptomics). Galaxy allows you to do analyses you cannot do anywhere else without the need to install or download anything. You can analyze multiple alignments, compare genomic annotations, profile metagenomic samples and much much more. Best of all, Galaxy''''s history system provides a complete analyses record that can be shared. Every history is an analysis workflow, which can be used to reproduce the entire experiment. The code for this Galaxy instance is available for download from BitBucket.
Proper citation: Stem Cell Discovery Engine (RRID:SCR_004453) Copy
http://cran.r-project.org/web/packages/kdetrees/
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.
Proper citation: Kdetrees (RRID:SCR_004522) Copy
http://snoopcgh.sourceforge.net/
A java desktop application for visualising and exploring comparative genomic hybridization (CGH) data.
Proper citation: SnoopCGH (RRID:SCR_004420) Copy
http://www.irisa.fr/symbiose/projects/gassst/
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.
Proper citation: GASSST (RRID:SCR_004413) Copy
A web server dedicated to the reconstruction of phylogenetic trees, reticulation networks and to the inference of horizontal gene transfer (HGT) events.
Proper citation: Tree and reticulogram REConstruction (RRID:SCR_004497) Copy
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