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A web-based software package for comparative genomics.
Proper citation: Sybil (RRID:SCR_005593) Copy
http://www.sanger.ac.uk/resources/software/lookseq/
A web-based application for alignment visualization, browsing and analysis of genome sequence data.
Proper citation: LookSeq (RRID:SCR_005625) Copy
http://zhanglab.c2b2.columbia.edu/index.php/OLego
A program specifically designed for de novo spliced mapping of mRNA-seq reads. It adopts a multiple-seed-and-extend scheme, and does not rely on a separate external mapper.
Proper citation: OLego (RRID:SCR_005811) Copy
http://cran.r-project.org/web/packages/aLFQ/
An R-package for estimating absolute protein quantities from label-free liquid chromatography tandem mass spectrometry (LC-MS/MS) proteomics data. It supports the commonly used absolute label-free protein abundance estimation methods (TopN, iBAQ, APEX, NSAF and SCAMPI) for LC-MS/MS proteomics data, quantifying on either MS1-, MS2-levels or spectral counts together with validation algorithms to enable automated data analysis and error estimation. Specifically, they used Monte-carlo cross-validation and bootstrapping for model selection and imputation of proteome-wide absolute protein quantity estimation.
Proper citation: aLFQ (RRID:SCR_005925) Copy
https://code.google.com/p/pepr-chip-seq/
A ChIP-Seq peak calling or differential binding analysis tool that is primarily designed for data with biological replicates. It uses a negative binomial distribution to model the read counts among the samples in the same group, and look for consistent differences between ChIP and control group or two ChIP groups run under different conditions.
Proper citation: PePr (RRID:SCR_005759) Copy
http://sourceforge.net/projects/dna-bison/
Allows users with access to a computer cluster to rapidly align whole-genome bisulfite sequencing or RRBS reads.
Proper citation: dna-bison (RRID:SCR_005913) Copy
http://www.bioinf.uni-freiburg.de/Software/GraphProt/
Software for modeling binding preferences of RNA-binding proteins from high-throughput experiments such as CLIP-seq and RNAcompete.
Proper citation: GraphProt (RRID:SCR_005842) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 20,2019.Database and analysis environment for experimentally determined binding sites of RNA-binding proteins. It supports the automatic functional annotation of short reads resulting primarily from crosslinking and immunoprecipitation experiments (CLIP) performed with RNA-binding proteins in order to identify the binding sites of these proteins. The functional annotation could be also applied to short reads resulting from other types of experiments such as mRNA-Seq, Digital Gene Expression, small RNA cloning, etc. The platform enables visualization and mining of individual data sets as well as analysis involving multiple experimental data sets. The platform can support collaborative projects involving multiple users and groups of users as well as public and private datasets.
Proper citation: CLIPZ (RRID:SCR_005755) Copy
http://apps.cytoscape.org/apps/jepetto
A Cytoscape plugin that performs integrated gene set analysis using information from interaction, pathways and processes databases. The plugin integrates information from three separate web servers specializing in enrichment analysis, pathways expansion and topological matching. It uses the TopoGSA server to identify topological analogies between the user selected gene set and the known pathways and processes. TopoGSA finds the most similar biological mechanism using the topological features of the interaction network of a user selected gene set. It is also able to suggest genes related to the query gene set using two pathway analysis servers EnrichNet and PathExpand. Both these servers are using a different topological matching algorithms that extends the query gene set with genes from the pathway databases. This integration substantially simplifies the analysis of user gene sets and the interpretation of the results.
Proper citation: JEPETTO (RRID:SCR_005909) Copy
A pattern growth algorithm based pileline for splice site detection in paired-end RNA-Seq data.
Proper citation: PASSion (RRID:SCR_005867) Copy
http://www-math.u-strasbg.fr/genpred/spip.php?article3
R software package to study, predict and simulate the diffusion of a signal through a temporal gene network. It predicts changes in gene expressions after a biological perturbation in the network and provides graphical outputs that allow monitoring the spread of a signal through the network., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: Cascade (RRID:SCR_005861) Copy
http://ftp://lausanne.isb-sib.ch/pub/databases/Bgee/general/IQRray.R
Software based on evolutionary conservation of expression profiles, implemented in R, for identification of poor quality arrays in dataset composed of arrays from many independent experiments.
Proper citation: IQRray (RRID:SCR_006057) Copy
http://cran.r-project.org/web/packages/YuGene/
Software providing a simple method for comparison of gene expression generated across different experiments, and on different platforms; that does not require global renormalization, and is not restricted to comparison of identical probes. YuGene works on a range of microarray dataset distributions, such as between manufacturers. The resulting output allows direct comparisons of gene expression between experiments and experimental platforms.
Proper citation: YuGene (RRID:SCR_006023) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 3rd,2023. A probabilistic algorithm that addresses the computational problems associated with aligning bisulfite sequencing data to a reference genome.
Proper citation: GNUMAP-BS (RRID:SCR_005995) Copy
http://www.bioconductor.org/packages/2.14/bioc/html/h5vc.html
Software package that contains functions to interact with tally data from Next-Generation Sequencing (NGS) experiments that is stored in HDF5 files.
Proper citation: h5vc (RRID:SCR_006039) Copy
https://bitbucket.org/cob87icW6z/cafe/wiki/Home
R software package for the detection of gross chromosomal abnormalities from gene expression microarray data.
Proper citation: CAFE (RRID:SCR_005983) Copy
http://sourceforge.net/projects/hiahia/
A sequence alignment tool to align both short and long reads to a reference genome. HIA has two indexes, a hash table index and a suffix array index. The hash table is capable of the direct lookup of a q-gram and the suffix array is very fast in the lookup of a variable length q-gram. Our experiments show that the hybrid of hash table and suffix array is useful at the perspective of speed to map NGS sequencing reads to a reference genome sequence.
Proper citation: HIA (RRID:SCR_006865) Copy
http://sourceforge.net/projects/fitgcp/
Software providing a framework for fitting mixtures of probability distributions to genome coverage profiles.
Proper citation: fitGCP (RRID:SCR_006741) Copy
http://www.niehs.nih.gov/research/resources/software/biostatistics/eagleview/
An information-rich viewer for next-generation genome assembles with data integration capability. EagleView can display a dozen different types of information including base qualities, machine specific trace signals, and genome feature annotations. It provides an easy way for inspecting visually the quality of a genome assembly and validating polymorphism candidate sites (e.g., SNPs) reported by polymorphism discovery tools. It can also facilitate data interpretation and hypothesis generation. EagleView is a multi-platform application developed with C++ and is available for all three major platforms: Windows, Linux, and Mac OS.
Proper citation: EagleView (RRID:SCR_006859) Copy
http://sourceforge.net/projects/gasic/
A method to correct read alignment results for the ambiguities imposed by similarities of genomes.
Proper citation: GASiC (RRID:SCR_006765) Copy
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