Tools   Select Another Resource Report Type

http://pga.mgh.harvard.edu/oligopicker/

Software to help selecting up to five oligo probes for each of the DNA sequences you provided for microarray spotting.

Proper citation: OligoPicker (RRID:SCR_008720) Copy   

•   Source: SciCrunch Registry

http://dc.crs4.it/projects/biodoop

A suite of parallel bioinformatics applications based upon a popular open-source Java implementation of MapReduce, Hadoop.

Proper citation: Biodoop (RRID:SCR_008711) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/drgap/

Designed to identify Driver Genes and Pathways in cancer genome sequencing studies.

Proper citation: DrGaP (RRID:SCR_008670) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/cancer/cga/invex/

A permutation-based method (written in Python) for ascertaining genes with a somatic mutation distribution showing evidence of positive selection for non-silent mutations.

Proper citation: InVEx (RRID:SCR_008734) Copy   

•   Source: SciCrunch Registry

http://cole-trapnell-lab.github.io/cufflinks/cuffmerge/

Software tool for transcriptome assembly and differential expression analysis for RNA-Seq. Includes script called cuffmerge that can be used to merge together several Cufflinks assemblies. It also handles running Cuffcompare as well as automatically filtering a number of transfrags that are likely to be artifacts. If the researcher has a reference GTF file, the researcher can provide it to the script to more effectively merge novel isoforms and maximize overall assembly quality.

Proper citation: Cufflinks (RRID:SCR_014597) Copy   

•   Source: SciCrunch Registry

http://libroadrunner.org/

Simulation engine for systems and synthetic biology to be used with other software applications. It retains the original functionality of RoadRunner but has changes in performance, back-end design, event handling, new C++ API, and stochastic simulation support.

Proper citation: libRoadRunner (RRID:SCR_014763) Copy   

•   Source: SciCrunch Registry

http://www.vicbioinformatics.com/software.prokka.shtml

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for the rapid annotation of prokaryotic genomes. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Prokka (RRID:SCR_014732) Copy   

•   Source: SciCrunch Registry

http://www.mybiosoftware.com/seaview-4-2-12-sequence-alignment-phylogenetic-tree-building.html

Graphical user interface for multiple sequence alignment and molecular phylogeny. SeaView also generates phylogenetic trees.

Proper citation: SeaView (RRID:SCR_015059) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/giira/

Gene prediction method that identifies potential coding regions based on the mapping of reads from an RNA-Seq experiment.

Proper citation: GIIRA (RRID:SCR_015507) Copy   

•   Source: SciCrunch Registry

http://great.stanford.edu/public/html/splash.php

Data analysis service that predicts functions of cis-regulatory regions identified by localized measurements of DNA binding events across an entire genome. Whereas previous methods took into account only binding proximal to genes, GREAT is able to properly incorporate distal binding sites and control for false positives using a binomial test over the input genomic regions. GREAT incorporates annotations from 20 ontologies and is available as a web application. The utility of GREAT extends to data generated for transcription-associated factors, open chromatin, localized epigenomic markers and similar functional data sets, and comparative genomics sets. Platform: Online tool

Proper citation: GREAT: Genomic Regions Enrichment of Annotations Tool (RRID:SCR_005807) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/Tools/pfa/iprscan/

Software package for functional analysis of sequences by classifying them into families and predicting presence of domains and sites. Scans sequences against InterPro's signatures. Characterizes nucleotide or protein function by matching it with models from several different databases. Used in large scale analysis of whole proteomes, genomes and metagenomes. Available as Web based version and standalone Perl version and SOAP Web Service.

Proper citation: InterProScan (RRID:SCR_005829) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/webservices/whatizit/info.jsf

A text processing system that allows you to do textmining tasks on text. It is great at identifying molecular biology terms and linking them to publicly available databases. Whatizit is also a Medline abstracts retrieval/search engine. Instead of providing the text by Copy&Paste, you can launch a Medline search. The abstracts that match your search criteria are retrieved and processed by a pipeline of your choice. Whatizit is also available as 1) a webservice and as 2) a streamed servlet. The webservice allows you to enrich content within your website in a similar way as in the wikipedia. The streamed servlet allows you to process large amounts of text.

Proper citation: Whatizit (RRID:SCR_005824) Copy   

•   Source: SciCrunch Registry

http://www.ibridgenetwork.org/wustl/splinter

Software that detects and quantifies short IN/DELs as well as single nucleotide substitutions in pooled-DNA samples.

Proper citation: SPLINTER (RRID:SCR_005826) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

http://genome.ucsc.edu/

Portal to interactively visualize genomic data. Provides reference sequences and working draft assemblies for collection of genomes and access to ENCODE and Neanderthal projects. Includes collection of vertebrate and model organism assemblies and annotations, along with suite of tools for viewing, analyzing and downloading data.

Proper citation: UCSC Genome Browser (RRID:SCR_005780) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/devel/bioc/html/SeqGSEA.html

Software package that provides methods for gene set enrichment analysis of high-throughput RNA-Seq data by integrating differential expression and splicing. It uses negative binomial distribution to model read count data, which accounts for sequencing biases and biological variation. Based on permutation tests, statistical significance can also be achieved regarding each gene''s differential expression and splicing, respectively.

Proper citation: SeqGSEA (RRID:SCR_005724) Copy   

•   Source: SciCrunch Registry

http://estscan.sourceforge.net/

ESTScan is a program that can detect coding regions in DNA sequences, even if they are of low quality. ESTScan will also detect and correct sequencing errors that lead to frameshifts. ESTScan is not a gene prediction program , nor is it an open reading frame detector. In fact, its strength lies in the fact that it does not require an open reading frame to detect a coding region. As a result, the program may miss a few translated amino acids at either the N or the C terminus, but will detect coding regions with high selectivity and sensitivity. ESTScan takes advantages of the bias in hexanucleotide usage found in coding regions relative to non-coding regions. This bias is formalized as an inhomogeneous 3-periodic fifth-order Hidden Markov Model (HMM). Additionally, the HMM of ESTScan has been extended to allows insertions and deletions when these improve the coding region statistics.

Proper citation: ESTScan (RRID:SCR_005742) Copy   

•   Source: SciCrunch Registry

https://array.nci.nih.gov/caarray/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on Sep 18, 2018. Open-source, web and programmatically accessible microarray data management system. caArray guides the annotation and exchange of array data using a federated model of local installations whose results are shareable across the cancer Biomedical Informatics Grid (caBIG). caArray furthers translational cancer research through acquisition, dissemination and aggregation of semantically interoperable array data to support subsequent analysis by tools and services on and off the Grid. As array technology advances and matures, caArray will extend its logical library of assay management.

Proper citation: caArray (RRID:SCR_006053) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/MetaQC/

Software for quality control and diagnosis for microarray meta-analysis. Quantitative quality control measures include: (1) internal homogeneity of co-expression structure among studies (internal quality control; IQC); (2) external consistency of co-expression structure correlating with pathway database (external quality control; EQC); (3) accuracy of differentially expressed gene detection (accuracy quality control; AQCg) or pathway identification (AQCp); (4) consistency of differential expression ranking in genes (consistency quality control; CQCg) or pathways (CQCp). For each quality control index, the p-values from statistical hypothesis testing are minus log transformed and PCA biplots were applied to assist visualization and decision. Results generate systematic suggestions to exclude problematic studies in microarray meta-analysis and potentially can be extended to GWAS or other types of genomic meta-analysis. The identified problematic studies can be scrutinized to identify technical and biological causes (e.g. sample size, platform, tissue collection, preprocessing etc) of their bad quality or irreproducibility for final inclusion / exclusion decision.

Proper citation: MetaQC (RRID:SCR_006000) Copy   

•   Source: SciCrunch Registry

http://bio-bigdata.hrbmu.edu.cn/diseasemeth/

Human disease methylation database. DiseaseMeth version 2.0 is focused on aberrant methylomes of human diseases. Used for understanding of DNA methylation driven human diseases.

Proper citation: DiseaseMeth (RRID:SCR_005942) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/bless-ec/

Software tool for Bloom-filter-based error correction for next-generation sequencing (NGS) reads. The algorithm produces accurate correction results with much less memory.

Proper citation: BLESS (RRID:SCR_005963) Copy   

•   Source: SciCrunch Registry