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http://www.compgen.org/tools/metagen
Software program providing a method for meta-analysis of case-control genetic association studies using random-effects logistic regression.
Proper citation: metagen (RRID:SCR_003443) Copy
http://sourceforge.net/projects/dnaclust/
Software program for clustering large number of short similar DNA sequences. It was originally designed for clustering targeted 16S rRNA pyrosequencing reads.
Proper citation: DNACLUST (RRID:SCR_001771) Copy
An open source data warehouse system built for the integration and analysis of complex biological data that enables the creation of biological databases accessed by sophisticated web query tools. Parsers are provided for integrating data from many common biological data sources and formats, and there is a framework for adding data. InterMine includes a user-friendly web interface that works "out of the box" and can be easily customized for specific needs, as well as a powerful, scriptable web-service API to allow programmatic access to data.
Proper citation: InterMine (RRID:SCR_001772) Copy
http://www.bioconductor.org/packages/release/bioc/html/unifiedWMWqPCR.html
Software package that implements the unified Wilcoxon-Mann-Whitney Test for qPCR data. This modified test allows for testing differential expression in qPCR data.
Proper citation: unifiedWMWqPCR (RRID:SCR_001706) Copy
http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm
THIS RESOURCE IS OUT OF SERVICE, documented on April 5, 2017, A software package for the analysis of ChIP-seq data with negative control., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CCAT (RRID:SCR_001843) Copy
https://urgi.versailles.inra.fr/Tools/S-Mart
Software toolbox that manages your RNA-Seq and ChIP-Seq data and also produces many different plots to visualize your data. It performs several tasks that are usually required during the analysis of mapped RNA-Seq and ChIP-Seq reads, including data selection and data visualization. It includes the selection (or the exclusion) of the data that overlaps with a reference set, clustering and comparative analysis. It also provides many ways to visualize data: size of the reads, density on the genome, distance with respect to a reference set, and the correlation of two data sets (with cloud plots). A computer science background is not required to run it through a graphical interface and it can be run on any personal computer, yielding results within an hour for most queries.
Proper citation: S-MART (RRID:SCR_001908) Copy
http://www.bioconductor.org/packages/release/bioc/html/SamSPECTRAL.html
Software that identifies cell population in flow cytometry data. It demonstrates significant advantages in proper identification of populations with non-elliptical shapes, low density populations close to dense ones, minor subpopulations of a major population and rare populations. It samples large data such that spectral clustering is possible while preserving density information in edge weights. More specifically, given a matrix of coordinates as input, SamSPECTRAL first builds the communities to sample the data points. Then, it builds a graph and after weighting the edges by conductance computation, the graph is passed to a classic spectral clustering algorithm to find the spectral clusters. The last stage of SamSPECTRAL is to combine the spectral clusters. The resulting connected components estimate biological cell populations in the data sample.
Proper citation: SamSPECTRAL (RRID:SCR_001858) Copy
http://www.bioconductor.org/packages/2.13/bioc/html/cqn.html
A normalization tool for RNA-Seq data, implementing the conditional quantile normalization method.
Proper citation: CQN (RRID:SCR_001786) Copy
http://www.bioconductor.org/packages/release/bioc/html/ADaCGH2.html
Software for analysis and plotting of array comparative genomic hybridization (CGH) data. It allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, BioHMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data.
Proper citation: ADaCGH2 (RRID:SCR_001981) Copy
https://cran.r-project.org/src/contrib/Archive/PurBayes/
An MCMC-based algorithm that uses next-generation sequencing data to estimate tumor purity and clonality for paired tumor-normal data.
Proper citation: PurBayes (RRID:SCR_002068) Copy
http://ribopicker.sourceforge.net/
Software to automatically identify and efficiently remove rRNA-like sequences from metatranscriptomic and metagenomic datasets.
Proper citation: riboPicker (RRID:SCR_000360) Copy
A software for genome assembly, and is specifically designed to analyze long Sanger-chemistry reads.
Proper citation: ARACHNE (RRID:SCR_000351) Copy
https://sites.google.com/site/beckerjeremie/home/nucleofinder
A software for a statistical approach for the detection of nucleosome positions in a cell population. The software identifies important features of nucleosome organization such as the spacing downstream of active promoters and the enrichment and depletion of GC/AT dinucleotides of in vitro nucleosomes.
Proper citation: NucleoFinder (RRID:SCR_000368) Copy
https://github.com/yongchao/flowPeaks
Software for fast and automatic clustering to classify the cells into subpopulations based on finding the peaks from the overall density function generated by K-means.
Proper citation: flowPeaks (RRID:SCR_000407) Copy
http://proteinprophet.sourceforge.net/
Software that automatically validates protein identifications made on the basis of peptides assigned to MS/MS spectra by database search programs such as SEQUEST.
Proper citation: ProteinProphet (RRID:SCR_000286) Copy
Software environment for maintaining databases of molecular sequences and additional information, and for analyzing the sequence data, with emphasis on phylogeny reconstruction. Programs have primarily been developed for ribosomal ribonucleic acid (rRNA) sequences and, therefore, contain special tools for alignment and analysis of these structures. However, other molecular sequence data can also be handled. Protein gene sequences and predicted protein primary structures as well as protein secondary structures can be stored in the same database. ARB package is designed for graphical user interface. Program control and data display are available in a hierarchical set of windows and subwindows. Majority of operations can be controlled using mouse for moving pointer and the left mouse button for initiating and performing operations.
Proper citation: ARB project (RRID:SCR_000515) Copy
Software tool for association study of high-dimensional microRNA expression data with repeated measures. The penalized regression model incorporates a grid search method for analyzing associations of high-dimensional microRNA expression data with repeated measures.
Proper citation: PGS (RRID:SCR_000475) Copy
Software package for noise-robust soft clustering of gene expression time-series data (including a graphical user interface)., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Mfuzz (RRID:SCR_000523) Copy
http://gmt.genome.wustl.edu/pindel/0.2.4/
Software to detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Pindel (RRID:SCR_000560) Copy
http://paleogenomics.irmacs.sfu.ca/FPSAC/
Sogftware for fast Phylogenetic Scaffolding of Ancient Contigs.
Proper citation: FPSAC (RRID:SCR_000555) Copy
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