Tools   Select Another Resource Report Type

http://bioconductor.org/packages/edgeR/

Bioconductor software package for Empirical analysis of Digital Gene Expression data in R. Used for differential expression analysis of RNA-seq and digital gene expression data with biological replication.

Proper citation: edgeR (RRID:SCR_012802) Copy   

•   Source: SciCrunch Registry
  

http://ciliate.org/index.php/home/welcome

TGD Wiki is a user-updatable database of information about the Tetrahymena thermophila genome sequence determined at The Institute for Genomic Research (TIGR). TGD Wiki provides information on the genome, genes, and proteins of Tetrahymena collected from the scientific literature, research community and many other resources. In order to keep the information in our database as current as possible, we will soon be inviting the members of the Tetrahymena community to add and update these annotations to reflect published research. TGD Wiki currently offers the following features: * Free, unrestricted read access to all available data * Sequence and annotation data for 24,725 genes (TIGR v.2008) * GBrowse genome browser with links to and from each gene page (TIGR v.2006) * BLAST searching of the TIGR gene models and genome sequence (TIGR v.2006) Tetrahymena Genome Database (TGD) Wiki began in 2004 at Stanford University using the schema and programs of its parent project, Saccharomyces Genome Database. TGD Wiki is now a collaboration between Bradley University, Stanford University, and Cornell University. As we begin TGD Wiki at its new home at Bradley University, the TGD Wiki database contains the following data from TGD: * Gene Names and Aliases * Gene Descriptions * Gene Ontology (GO) Annotations * Homologs (similar genes in selected organisms) * Protein Domains * Associated Literature * Paragraphs (longer, free-text descriptions of gene function, structure, and significance) * Coding and Protein Sequences We have updated the following fields to match the newest gene model sequences (TIGR v.2008): Coding and Protein Sequences, Protein Domains and Gene Descriptions. We will also be recalculating the GO Annotations (IEA evidence code) and Homologs as part of our effort to keep the annotations in TGD Wiki as current as possible. We will be relying on members of the Tetrahymena community to maintain high-quality, updated annotations in the remainder of the fields using our annotation interface. Also setting up new database superdb - for unpublished data Look at Ciliate.org for news on this and other new databases

Proper citation: TGD (RRID:SCR_012803) Copy   

•   Source: SciCrunch Registry
  

http://www.scienceexchange.com/facilities/university-of-toledo

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on April 15,2024. Portal, Core facility

Proper citation: University of Toledo Labs and Facilities (RRID:SCR_012493) Copy   

•   Source: SciCrunch Registry
  

https://www.q2labsolutions.com/genomics-laboratories

Core provides whole genome to focused set gene expression and genotyping assays along with DNA sequencings services, sequence enrichment technologies and bioinformatics support. Platforms utilized include Affymetrix GeneChip, Agilent Sure Select, Fluidigm Access Arrays, Illumina BeadChip, iScan, Genome Analyzer and Hi-Seq, RainDance Technologies RDT 1000 and, the Pacific Biosciences PacBio RS. Expression Analysis offers solutions for challenging specimens such as whole blood and FFPE tissues, as well as nucleic acid isolation and data analysis services.

Proper citation: Q Squared Solutions Expression Analysis (RRID:SCR_012497) Copy   

•   Source: SciCrunch Registry
  

http://bioconductor.org/packages/release/bioc/html/DNaseR.html

A R package that enables the identification of protein binding footprints in DNase I hypersensitive sites sequencing (DNase-seq) data.

Proper citation: DNaseR (RRID:SCR_012819) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/release/bioc/html/tRanslatome.html

Detection of differentially expressed genes (DEGs) from the comparison of two biological conditions among different levels of gene expression, using several statistical methods: Rank Product, t-test, SAM, Limma, ANOTA, DESeq, edgeR.

Proper citation: tRanslatome (RRID:SCR_012810) Copy   

•   Source: SciCrunch Registry
  

https://sites.google.com/site/oncosnp/

An analytical software tool for characterizing copy number alterations and loss-of-heterozygosity (LOH) events in cancer samples from SNP genotyping data.

Proper citation: OncoSNP (RRID:SCR_012985) Copy   

•   Source: SciCrunch Registry
  

http://www.mmc.edu/

Founded in 1876, Meharry is a non-profit university in Tennessee. Meharry includes a medical school, dental school, and a graduate school.

Proper citation: Meharry Medical College (RRID:SCR_012863) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/2.12/bioc/html/RLMM.html

A Genotype Calling Algorithm for Affymetrix SNP Arrays.

Proper citation: RLMM (RRID:SCR_012984) Copy   

•   Source: SciCrunch Registry
  

https://github.com/bedops/bedops

A suite of tools to address common questions raised in genomic studies - mostly with regard to overlap and proximity relationships between data sets.

Proper citation: BEDOPS (RRID:SCR_012865) Copy   

•   Source: SciCrunch Registry
  

http://www.zebrafinchatlas.org

Expression atlas of in situ hybridization images from large collection of genes expressed in brain of adult male zebra finches. Goal of ZEBrA project is to develop publicly available on-line digital atlas that documents expression of large collection of genes within brain of adult male zebra finches.

Proper citation: Zebra Finch Expression Brain Atlas (RRID:SCR_012988) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/ibdld/

A C++ software program for multipoint IBD estimation based on high density SNP genotype data.

Proper citation: IBDLD (RRID:SCR_013043) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/solsnp/

A Java-based DNA variant calling tool for Next-Generation Sequencing alignment data.

Proper citation: SolSNP (RRID:SCR_013045) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/tumorhats/

A software tool that calls the amplified alleles, and thus amplified haplotype, in copy number aberration regions in next generation sequencing tumor data.

Proper citation: HATS (RRID:SCR_013044) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/2.12/bioc/html/charm.html

Software package that implements analysis tools for DNA methylation data generated using Nimblegen microarrays and the McrBC protocol.

Proper citation: charm (RRID:SCR_012992) Copy   

•   Source: SciCrunch Registry
  

http://gmod.org/wiki/Flash_GViewer

Flash GViewer is a customizable Flash movie that can be easily inserted into a web page to display each chromosome in a genome along with the locations of individual features on the chromosomes. It is intended to provide an overview of the genomic locations of a specific set of features - eg. genes and QTLs associated with a specific phenotype, etc. rather than as a way to view all features on the genome. The features can hyperlink out to a detail page to enable to GViewer to be used as a navigation tool. In addition the bands on the chromosomes can link to defineable URL and new region selection sliders can be used to select a specific chromosome region and then link out to a genome browser for higher resolution information. Genome maps for Rat, Mouse, Human and C. elegans are provided but other genome maps can be easily created. Annotation data can be provided as static text files or produced as XML via server scripts. This tool is not GO-specific, but was built for the purpose of viewing GO annotation data. Platform: Online tool

Proper citation: Flash Gviewer (RRID:SCR_012870) Copy   

•   Source: SciCrunch Registry
  

http://sourceforge.net/projects/chipotle-perl/

A peak-finding algorithm used to analyze ChIP-chip microarray data.

Proper citation: ChIPOTle Peak Finder (RRID:SCR_012991) Copy   

•   Source: SciCrunch Registry
  

http://www.siu.edu/

Public research university in Carbondale, Illinois. Founded in 1869, SIU is the oldest campus of the Southern Illinois University system.

Proper citation: Southern Illinois University; Illinois; USA (RRID:SCR_012873) Copy   

•   Source: SciCrunch Registry
  

http://rnaseq-mats.sourceforge.net/

Software tool to detect differential alternative splicing events from RNA-Seq data. Calculates P value and false discovery rate that difference in isoform ratio of gene between two conditions exceeds given user defined threshold. Can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. Handles replicate RNA-Seq data from both paired and unpaired study design.

Proper citation: Multivariate Analysis of Transcript Splicing (RRID:SCR_013049) Copy   

•   Source: SciCrunch Registry
  

http://www.bioconductor.org/packages/2.12/bioc/html/BiSeq.html

Software package that provides useful classes and functions to handle and analyze targeted bisulfite sequencing (BS) data such as reduced-representation bisulfite sequencing (RRBS) data.

Proper citation: BiSeq (RRID:SCR_012993) Copy   

•   Source: SciCrunch Registry