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on page 1 showing 20 out of 36 results

    BAMseek

Cite this (BAMseek, RRID:SCR_000672)

URL: https://code.google.com/p/bamseek/

Resource Type: Resource, data visualization software, software application, data processing software, software resource

A Large File Viewer for BAM and SAM alignment files.

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    Bridger

Cite this (Bridger, RRID:SCR_017039)

URL: https://github.com/fmaguire/Bridger_Assembler

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software package as de novo trascriptome assembler for RNA-Seq data. Can assemble all transcripts from short reads without using reference. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux.

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Cite this (ChIPseeqer, RRID:SCR_001545)

URL: http://physiology.med.cornell.edu/faculty/elemento/lab/chipseq.shtml

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

Software that provides a comprehensive framework for the analysis of ChIP-seq data.

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Cite this (ChIPSeq Peak Finder, RRID:SCR_002081)

URL: http://cmb.gis.a-star.edu.sg/ChIPSeq/paperChIPSeq.htm

Resource Type: Resource, software resource, software application, data analysis software, data processing software

THIS RESOURCE IS OUT OF SERVICE, documented on April 12, 2017. A software tool to find peaks from ChIPSeq data generated from the Solexa/Illumina platform.

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Cite this (CLC Genomics Workbench, RRID:SCR_011853)

URL: http://www.clcbio.com/products/clc-genomics-workbench/

Resource Type: Resource, software resource, software application, data analysis software, data processing software, data visualization software

Commercially available software for visualization and analysis of next generation sequencing data. Used for viewing, exploring, and sharing of NGS analysis results. Complete toolkit for genomics, transcriptomics, epigenomics, and metagenomics in one program.

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Cite this (Computational Suite for Bioinformaticians and Biologists, RRID:SCR_017234)

URL: https://github.com/csbbcompbio/CSBB-v3.0

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software package for analysis of sequencing data. Command line based bioinformatics suite to analyze biological data acquired through biological experiments.

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    CorMut

Cite this (CorMut, RRID:SCR_000053)

URL: http://bioconductor.org/packages/release/bioc/html/CorMut.html

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

A software package for computing correlated mutations based on selection pressure. Three methods are provided for detecting correlated mutations, including conditional selection pressure, mutual information and Jaccard index. The computation consists of two steps: First, the positive selection sites are detected; second, the mutation correlations are computed among the positive selection sites. Note that the first step is optional. Meanwhile, CorMut facilitates the comparison of the correlated mutations between two conditions by the means of correlated mutation network.

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    fermi

Cite this (fermi, RRID:SCR_016652)

URL: https://github.com/lh3/fermi

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

Software assembler and analysis tool for whole-genome short-gun sequencing for Illumina reads. Provides tools for error correction, sequence-to-read alignment and comparison between read sets. Used for large genomes.

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    GeneMeta

Cite this (GeneMeta, RRID:SCR_001201)

URL: http://www.bioconductor.org/packages/release/bioc/html/GeneMeta.html

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software package providing a collection of meta-analysis tools for analysing high throughput experimental data.

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Cite this (GeneNetworkBuilder, RRID:SCR_006455)

URL: http://www.bioconductor.org/packages/devel/bioc/html/GeneNetworkBuilder.html

Resource Type: Resource, software resource, software application

Software application for discovering direct or indirect targets of transcription factors (TFs) using ChIP-chip or ChIP-seq, and microarray or RNA-seq gene expression data. Inputting a list of genes of potential targets of one TF from ChIP-chip or ChIP-seq, and the gene expression results, it generates a regulatory network of the TF.

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    HOMER

Cite this (HOMER, RRID:SCR_010881)

URL: http://homer.ucsd.edu/

Resource Type: Resource, software resource, software application, sequence analysis software, data analysis software, data processing software

Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++.

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    Jmosaics

Cite this (Jmosaics, RRID:SCR_001094)

URL: http://www.bioconductor.org/packages/2.12/bioc/html/jmosaics.html

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

R software that detects enriched regions of ChIP-seq data sets jointly.

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    metaSeq

Cite this (metaSeq, RRID:SCR_000056)

URL: http://www.bioconductor.org/packages/release/bioc/html/metaSeq.html

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software package for meta-analysis of RNA-Seq count data in multiple studies. The probabilities by one-sided NOISeq are combined by Fisher's method or Stouffer's method.

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Cite this (Mutascope, RRID:SCR_001265)

URL: http://sourceforge.net/projects/mutascope/

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software suite to analyze data from high throughput sequencing of PCR amplicons, with an emphasis on normal-tumor comparison for the accurate and sensitive identification of low prevalence mutations.

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Cite this (Mutation Surveyor, RRID:SCR_001247)

URL: http://www.softgenetics.com/mutationSurveyor.php

Resource Type: Resource, software resource, software application, sequence analysis software, data analysis software, data processing software

Software for DNA sequencing analysis that integates with Sanger Sequencing files generated by Applied Biosystems Genetic Analyzers, MegaBACE, and Beckman CEQ electrophoresis systems. It can be used to find single nucleotide polymorphisms (SNPs), insertions and deletions (INDELS), and somatic mutations in direct sequencing, PCR sequencing, mitochondrial DNA sequencing, and resequencing projects.

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    NanoFilt

Cite this (NanoFilt, RRID:SCR_016966)

URL: https://github.com/wdecoster/nanofilt

Resource Type: Resource, software resource, software application, data processing software

Software tool written in Python to perform its filtering based on mean read quality and GC content and read length. Used for filtering and trimming of long read sequencing data.

  • From Current Category

Cite this (OmicsSIMLA, RRID:SCR_017011)

URL: https://omicssimla.sourceforge.io

Resource Type: Resource, software resource, software application, simulation software, software toolkit

Software tool for generating multi omics data with disease status. Simulates genomics (SNPs and copy number variations), epigenomics ( whole genome bisulphite sequencing), transcriptomics ( RNA seq), and proteomics (normalized reverse phase protein array) data at the whole genome level. Available as desktop and web application version.

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    RaceID

Cite this (RaceID, RRID:SCR_017045)

URL: https://github.com/dgrun/RaceID

Resource Type: Resource, software resource, software application, algorithm resource, data processing software, data analysis software

Algorithm for identification of rare and abundant cell types from single cell transcriptome data. Based on transcript counts obtained with unique molecular identifies. Used for discovering rare cell types and corresponding marker genes in healthy and diseased organs. Operating system Unix/Linux, Mac OS, Windows.

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    rGADEM

Cite this (rGADEM, RRID:SCR_001091)

URL: http://www.bioconductor.org/packages/2.12/bioc/html/rGADEM.html

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

R package with tools for de novo motif discovery in large-scale genomic sequence data.

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    sabre

Cite this (sabre, RRID:SCR_011843)

URL: https://github.com/najoshi/sabre

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software tool to demultiplex barcoded reads into separate files. Works on both single-end and paired-end data in fastq format. Used in next generation sequencing to analyze a broad range of data.

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