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on page 1 showing 20 out of 184 results

Cite this (AbundantOTU+, RRID:SCR_016527)

URL: http://omics.informatics.indiana.edu/AbundantOTU/

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

Software tool for analysis of large 16S rRNA pyrosequences by using a consensus alignment algorithm, utilizing the sequence redundancy of abundant species in the pyrosequence dataset.

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Cite this (AdapterRemoval, RRID:SCR_011834)

URL: https://github.com/MikkelSchubert/adapterremoval

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

Software program to remove residual adapter sequences from next generation sequencing reads.

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Cite this (Agilent Masshunter Qualitative Analysis, RRID:SCR_016657)

URL: https://www.agilent.com/en/products/software-informatics/masshunter-suite/masshunter-qualitative-analysis-gcms

Resource Type: Resource, data analysis software, data processing software, software application, data analytics software, software toolkit, software resource, data acquisition software

Software tools for compound-centric data mining and navigation. Used to identify compounds in overlapping and co-eluting peaks with feature extraction and correlation algorithms for chromatographic separation. Used for separating true signals from noise.

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    ANDES

Cite this (ANDES, RRID:SCR_002791)

URL: http://andestools.sourceforge.net/

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

Software library and a suite of applications, written in Perl and R, for deep sequencing statistical analyses.

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    asSeq

Cite this (asSeq, RRID:SCR_001625)

URL: http://bios.unc.edu/~weisun/software/asSeq.htm

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

Software that establishes a statistical framework for future developments of eQTL (expression quantitative trait locus) mapping methods using RNA-seq data (e.g., linkage-based eQTL mapping), and the joint study of multiple genetic markers and/or multiple genes. This R package has been submitted to R/bioconductor. It will be available on bioconductor soon. It is recommended to install this R package from bioconductor. You can also install this R package from the source code by yourself. Since the R package contains C code, a C complier is required for installation. With both R and appropriate c complier installed, this R package can be installed using the following command (in Mac Terminal window or Windows command window) R CMD INSTALL asSeq

  • From Current Category

Cite this (AutoAssemblyD, RRID:SCR_001087)

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

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

Software which performs local and remote genome assembly by several assemblers based on an XML Template which can replace the large command lines required by most assemblers.

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    Babel

Cite this (Babel, RRID:SCR_004307)

URL: http://taylorlab.ucsf.edu/software_data.html

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

Software that implements babel routines for identifying unusual ribosome protected fragment counts given mRNA counts

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    BAC

Cite this (BAC, RRID:SCR_001067)

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

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

R software package that uses a Bayesian hierarchical model to detect enriched regions from ChIP-chip experiments.

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    BAIT

Cite this (BAIT, RRID:SCR_000511)

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

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

Software to create strand inheritance plots in data derived from the Strand-Seq sequencing protocol. The software is designed to be flexible with a range of species, and basic template folders can called to read in species-specific data.

  • From Current Category

    bamova

Cite this (bamova, RRID:SCR_000510)

URL: http://www.uwyo.edu/buerkle/software/bamova/

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

Software that implements a Bayesian Analysis of Molecular Variance and different likelihood models for three different types of molecular data (including two models for high throughput sequence data).

  • From Current Category

Cite this (BinPacker, RRID:SCR_017038)

URL: https://github.com/macmanes-lab/BinPacker/blob/master/README

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

Software tool as de novo trascriptome assembler for RNA-Seq data. Used to assemble full length transcripts by remodeling problem as tracking set of trajectories of items over splicing graph. 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 (Biometric Research Branch: ArrayTools, RRID:SCR_000778)

URL: http://linus.nci.nih.gov./BRB-ArrayTools.html

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

A software package for the visualization and statistical analysis of DNA microarray gene expression data. The tools have been developed from the R statistical system, in C and fortran programs and Java applications. They are integrated into Excel as an add-in.

  • From Current Category

    BlackOPs

Cite this (BlackOPs, RRID:SCR_000032)

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

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

Software used to characterize the mappability of RNA-Seq reads and create a blacklist of genomic positions of mismapped reads. This blacklist is used to filter potential false positives from variant or RNA editing calls.

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    BLESS

Cite this (BLESS, RRID:SCR_005963)

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

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

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

  • From Current Category

    Bowtie

Cite this (Bowtie, RRID:SCR_005476)

URL: http://bowtie-bio.sourceforge.net/index.shtml

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

Software tool for aligning short DNA sequences to large genomes. Bowtie 2 supports gapped, local, and paired end alignment modes.

  • From Current Category

    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.

  • From Current Category

Cite this (BSmooth-align, RRID:SCR_000013)

URL: https://github.com/BenLangmead/bsmooth-align

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

A statistics and alignment pipeline software that performs the alignment of bisulfite sequence reads and tabulates read-level methylation measurements.

  • From Current Category

Cite this (BS Seeker, RRID:SCR_005641)

URL: http://pellegrini.mcdb.ucla.edu/BS_Seeker/BS_Seeker.html

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

Software which performs accurate and fast mapping of bisulfite-treated short reads. Supplementary information and examples are provided on the site.

  • From Current Category

    bsseq

Cite this (bsseq, RRID:SCR_001072)

URL: http://www.bioconductor.org/packages/2.13/bioc/html/bsseq.html

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

R package with tools for analyzing and visualizing bisulfite sequencing data.

  • From Current Category

    BWA

Cite this (BWA, RRID:SCR_010910)

URL: http://bio-bwa.sourceforge.net/

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

Software for aligning sequencing reads against large reference genome. Consists of three algorithms: one for sequence reads up to 100bp, and other two for longer sequences ranged from 70bp to 1Mbp.

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