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http://obi-warp.sourceforge.net/
Software that aligns matrices along a single axis using Dynamic Time Warping (DTW) and a one-to-one (bijective) interpolated warp function.
Proper citation: OBI-Warp (RRID:SCR_012041) Copy
Software providing a data analysis pipeline for shotgun mass-spectrometry proteomics.
Proper citation: CPFP (RRID:SCR_012043) Copy
http://sourceforge.net/projects/icplquant/
A proteomics software tool for quantitatively analyzing large mass spectrometric datasets acquired from ICPL based proteomics experiments.
Proper citation: ICPL ESIQuant (RRID:SCR_012047) Copy
http://www.bioconductor.org/packages/2.11/bioc/html/easyRNASeq.html
Software that calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as ''RPKM'' or by the ''DESeq'' or ''edgeR'' package.
Proper citation: easyRNASeq (RRID:SCR_012020) Copy
http://sourceforge.net/projects/nailsystemsbiology/
A set of software tools to simplify the range of computational activities involved in regulatory network inference. It is technology-independent and includes an interface layer to allow easy integration of components into other applications. It is implemented in MATLAB and is available for all researchers to use.
Proper citation: NAIL (RRID:SCR_012134) Copy
https://code.google.com/p/localali/
A fast and scalable local network alignment software tool for the identification of functionally conserved modules in multiple networks. LocalAli outperforms all existing algorithms in terms of coverage, consistency and scalability, meanwhile retains a high precision in the identification of functionally coherent subnetworks.
Proper citation: LocalAli (RRID:SCR_012147) Copy
Whole genome secondary analysis on Illumina sequencing platforms.
Proper citation: Isaac (RRID:SCR_012772) Copy
http://sift.bii.a-star.edu.sg/
Data analysis service to predict whether an amino acid substitution affects protein function based on sequence homology and the physical properties of amino acids. SIFT can be applied to naturally occurring nonsynonymous polymorphisms and laboratory-induced missense mutations. (entry from Genetic Analysis Software) Web service is also available.
Proper citation: SIFT (RRID:SCR_012813) Copy
http://bioconductor.org/packages/release/bioc/html/lumi.html
Software that provides an integrated solution for the Illumina microarray data analysis.
Proper citation: lumi (RRID:SCR_012781) Copy
Software tool as plugin powered hybrid computing platform for deploying deep learning applications such as advanced image analysis tools. Runs on mobile and desktop environment cross different operating systems, can run in the browser, localhost, remote and cloud servers.
Proper citation: ImJoy (RRID:SCR_020935) Copy
http://srna-workbench.cmp.uea.ac.uk
Software package for analysing small RNA data. Software suite of tools for analyzing miRNAs and sRNAs. Performs analysis of single or multiple sample small RNA datasets from both plants and animals.
Proper citation: UEA sRNA Workbench (RRID:SCR_020947) Copy
https://bioconductor.org/packages/release/bioc/html/PhenStat.html
Software R package for statistical analysis of phenotypic data.Tool kit for standardized analysis of high throughput phenotypic data.
Proper citation: PhenStat (RRID:SCR_021317) Copy
http://www-personal.umich.edu/~jianghui/rseq/
A software toolkit for RNA sequence data analysis. It contains programs that cover several aspects of RNA-Seq data analysis such as read quality assessment, reference sequence generation, sequence mapping, and gene and isoform expressions estimations.
Proper citation: rSeq (RRID:SCR_000562) Copy
A database dedicated to the collection and classification of mobile genetic elements (MGEs) from various sources, comprising all known phage genomes, plasmids and transposons. In addition to provide information on the full genomes and genetic entities, it aims at building a comprehensive classification of the functional modules of MGE's at the protein, gene, and higher levels. Prophinder, a tool dedicated to the detection of prophages in sequenced bacterial genomes, is available on ACLAME.
Proper citation: A Classification of Mobile genetic Elements (RRID:SCR_001694) Copy
https://services.healthtech.dtu.dk/services/DictyOGlyc-1.1/
Server that produces neural network predictions for GlcNAc O-glycosylation sites in Dictyostelium discoideum proteins.
Proper citation: DictyOGlyc (RRID:SCR_001600) Copy
http://www.glycosciences.de/modeling/glyprot/
Web-based tool that enables meaningful N-glycan conformations to be attached to all the spatially accessible potential N-glycosylation sites of a known three-dimensional (3D) protein structure. The 3D structure of protein is required as input. Potential N-glysylations site are automatically detected. The attached glycan are constructed with SWEET-II, http://www.glycosciences.de/modeling/sweet2/doc/index.php
Proper citation: GlyProt (RRID:SCR_001560) Copy
Database of experimentally verified phosphorylation sites in eukaryotic proteins. Entries are manually curated with links to literature references, information about structure, interaction partners and sub-cellular compartment tissues, and sequences from the UniProt database.
Proper citation: Phospho.ELM (RRID:SCR_001109) Copy
http://hipipe.ncgm.sinica.edu.tw/
Tool that provides high performance NGS (next-generation sequencing) data analysis pipelines so that researchers with minimum IT or bioinformatics knowledge can perform common analyses on NGS data. 3 TB of storage space is reserved for each task.
Proper citation: HiPipe (RRID:SCR_001215) Copy
Database for conserved sequence motifs identified by genome scale motif discovery, similarity, clustering, co-occurrence and coexpression calculations. Sequence inputs include low-coverage genome sequence data and ENCODE data. The database offers information on atomic motifs, motif groups and patterns. In promoter-based cisRED databases, sequence search regions for motif discovery extend from 1.5 Kb upstream to 200b downstream of a transcription start site, net of most types of repeats and of coding exons. Many transcription factor binding sites are located in such regions. For each target gene's search region, a base set of probabilistic ab initio discovery tools is used, in parallel, to find over-represented atomic motifs. Discovery methods use comparative genomics with over 40 vertebrate input genomes. In ChIP-seq-based cisRED databases, sequence search regions for motif discovery correspond to significant peaks that represent genome-wide sites of protein-DNA binding. Because such peaks occur in a wide range of genic and intergenic locations, ChIP-seq and promoter-based databases are complementary. Currently, motif discovery for ChIP-seq data uses scan-based approaches that make more explicit use of sets of sequences known to be functional transcription factor binding sites, and that consider a wide range of levels of conservation. For the human STAT1 ChIP-seq database search regions in the target species (human) was selected +/- 300 bp around the ChIP-seq peak maximum. Repeats and coding regions were masked. Multiple sequence alignment were used to assemble orthologous input sequences from other species.
Proper citation: cisRED: cis-regulatory element (RRID:SCR_002098) Copy
Reference database and analysis platform for corynebacterial transcription factors and gene regulatory networks. It generates links to genome annotations, to identified transcription factors and to the corresponding cis-regulatory elements. CoryneRegNet is based on a multi-layered, hierarchical and modular concept of transcriptional regulation and was implemented by using the relational database management system MySQL and an ontology-based data structure.
Proper citation: CoryneRegNet (RRID:SCR_002255) Copy
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