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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
http://research-public.gene.com/Research/genentech/canpredict/index.html
Web application that uses a combination of computational methods to identify those changes most likely to be cancer-associated.
Proper citation: CanPredict (RRID:SCR_008216) Copy
Data analysis service that allows to process CEL files from Affymetrix, Inc. GeneChip Gene 1.0 ST Arrays to identify alternative splicing.
Proper citation: Gene Array Analyzer (RRID:SCR_008323) Copy
http://dario.bioinf.uni-leipzig.de/index.py
A free web server for the analysis of short RNAs from high throughput sequencing data.
Proper citation: DARIO (RRID:SCR_008600) Copy
http://array.mbb.yale.edu/analysis/
A fully integrated platform for processing microarray data.
Proper citation: ExpressYourself (RRID:SCR_008881) Copy
Blog presenting news and information, and spur discussion about topics related to RNA-Seq.
Proper citation: RNA-Seq Blog (RRID:SCR_010025) Copy
http://bioinfo1.uni-plovdiv.bg/isomiRex/
A web tool for the identification of microRNAs and their isomiRs, as well as differential expression from NGS datasets.
Proper citation: isomiRex (RRID:SCR_009521) Copy
http://cbdb.nimh.nih.gov/microsniper/
A web-based application which predicts the impact of a SNP on putative microRNA targets.
Proper citation: MicroSNiPer (RRID:SCR_009880) Copy
http://centre.bioinformatics.zj.cn/mirtools/
A comprehensive web server developed to allow researchers to comprehensively characterize small RNA transcriptome.
Proper citation: mirTools (RRID:SCR_009701) Copy
http://diana.imis.athena-innovation.gr/DianaTools/index.php?r=lncBase/index
Database that hosts elaborated information for both predicted and experimentally verified, miRNA-lncRNA interactions. The database consists of two distinct modules. The Experimental Module contains detailed information for more than 5,000 interactions, between 2,958 lncRNAs and 120 miRNAs, ranging from miRNA and lncRNA related facts to information specific to their interaction, the experimental validation methodologies and their outcomes. The Prediction Module, which is based on the latest version of DIANA-microT target prediction algorithm (DIANA-microT-CDS), contains detailed information for more than 10 million interactions, between 56,097 lncRNAs and 3,078 miRNAs, ranging from miRNA and lncRNA related details to specific information regarding their interaction sites, graphical representation of their binding and the predicted score. This module exhibits a unique feature for searching the database. Users are able to add genomic locations to their queries thus browsing every miRNA-lncRNA interaction that has at least one MRE located inside the queried locus.
Proper citation: DIANA-LncBase (RRID:SCR_010840) Copy
Database serving as a tool for microRNA target prediction. The HOCTAR procedure is based on the integration of expression profiling and sequence-based miRNA target recognition softwares. HOCTAR database (db) is the first and unique database to use transcriptomic data to score putative miRNA targets looking at the expression behaviour of their host genes, and it includes and re-analyzes all miRNA target predictions generated by softwares such as miRanda, TargetScan and PicTar. The HOCTARdb contains the prediction target lists for 290 human intragenic miRNAs and also provides tentative assignments of miRNA function based on Gene Ontology analyses of their predicted targets. There are two ways to interrogate HOCTARdb: (i) by selecting a miRNA using either an alphabetically sorted pull-down menu in the microRNA query, or (ii) by typing a target gene symbol (HUGO Gene Name-approved) in the Target Gene Name query.
Proper citation: HOCTAR (RRID:SCR_010842) Copy
http://www.ebi.ac.uk/enright-srv/microcosm/htdocs/targets/v5/
Database of computationally predicted targets for microRNAs across many species.
Proper citation: MicroCosm Targets (RRID:SCR_010846) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 6th,2023. Software genome database management system.
Proper citation: AceDB (RRID:SCR_010671) Copy
http://mimirna.centenary.org.au/mireval/
A web tool for simple microRNA prediction in genome sequences.
Proper citation: miREval (RRID:SCR_010830) Copy
A collaborative project to better understand the relationship between genotype and phenotype in humans that connects human phenotype and clinical data in various locus-specific mutation databases (LSDBs) with data on genome sequences, evolutionary history, and function in the UCSC Genome Browser. PhenCode is a collaboration among researchers at Penn State, UC Santa Cruz, and locus experts at other institutions.
Proper citation: PhenCode (RRID:SCR_010799) Copy
http://159.149.160.51/pscan_chip_dev/
Web server that, starting from a collection of genomic regions derived from a ChIP-Seq experiment, scans them using motif descriptors like JASPAR or TRANSFAC position-specific frequency matrices, or descriptors uploaded by users, and it evaluates both motif enrichment and positional bias within the regions according to different measures and criteria.
Proper citation: Pscan-ChIP (RRID:SCR_010885) Copy
http://www.unc.edu/~yunmli/1000G-imp/
A comprehensive SNP and indel imputability database.
Proper citation: SNP and indel Imputability (RRID:SCR_010800) Copy
A tool to predict changes in protein stability upon point mutations.
Proper citation: CUPSAT (RRID:SCR_010773) Copy
http://ls-snp.icm.jhu.edu/ls-snp-pdb/
A web tool for genome-wide annotation of human SNPs.
Proper citation: LS-SNP/PDB (RRID:SCR_010774) Copy
http://legumetfdb.psc.riken.jp/
A public database that provides predicted transcription factor (TF) encoding genes annotated in genome sequences of three major legume species: soybean (Glycine max), Lotus japonicus and Medicago truncatula.
Proper citation: LegumeTFDB (RRID:SCR_010896) Copy
http://bleoberis.bioc.cam.ac.uk/mcsm
Data analysis service to the study of missense mutations which relies on graph-based signatures.
Proper citation: mCSM (RRID:SCR_010776) Copy
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