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on page 1 showing 20 out of 203 results from 1 sources

    ABIDE

Cite this (ABIDE, RRID:SCR_003612)

URL: http://fcon_1000.projects.nitrc.org/indi/abide/

Resource Type: Resource, data set, data or information resource

Resting state functional magnetic resonance imaging (R-fMRI) datasets from 539 individuals with autism spectrum disorder (ASD) and 573 typical controls. This initiative involved 16 international sites, sharing 20 samples yielding 1112 datasets composed of both MRI data and an extensive array of phenotypic information common across nearly all sites. This effort is expected to facilitate discovery science and comparisons across samples. All datasets are anonymous, with no protected health information included.

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Cite this (ABS filter, RRID:SCR_005328)

URL: http://updepla1srv1.epfl.ch/waszaks/absfilter/

Resource Type: Resource, software resource

R package for identification and removal of low-complexity sites in allele-specific analysis of ChIP-seq data.

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Cite this (Academic Seismic Portal at LDEO, RRID:SCR_002194)

URL: http://www.marine-geo.org/portals/seismic/

Resource Type: Resource, data or information resource, database

Seismic Reflection Field Data from the academic research community. Their partner Academic Seismic Portal at UTIG offers additional seismic resources, http://www.ig.utexas.edu/sdc/

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    ADaCGH2

Cite this (ADaCGH2, RRID:SCR_001981)

URL: http://www.bioconductor.org/packages/release/bioc/html/ADaCGH2.html

Resource Type: Resource, software resource

Software for analysis and plotting of array comparative genomic hybridization (CGH) data. It allows usage of Circular Binary Segementation, wavelet-based smoothing (both as in Liu et al., and HaarSeg as in Ben-Yaacov and Eldar), HMM, BioHMM, GLAD, CGHseg. Most computations are parallelized (either via forking or with clusters, including MPI and sockets clusters) and use ff for storing data.

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    ALDEx2

Cite this (ALDEx2, RRID:SCR_003364)

URL: https://github.com/ggloor/ALDEx2

Resource Type: Resource, software resource

Software tool to examine compositional high-throughput sequence data with Welch's t-test. A differential relative count abundance analysis for the comparison of two conditions. For example, single-organism and meta-rna-seq high-throughput sequencing assays, or of selected and unselected values from in-vitro sequence selections. Uses a Dirichlet-multinomial model to infer abundance from counts, that has been optimized for three or more experimental replicates. Infers sampling variation and calculates the expected Benjamini-Hochberg false discovery rate given the biological and sampling variation using several parametric and non-parametric tests. Can to glm and Kruskal-Wallace tests on one-way ANOVA style designs.

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    aldex

Cite this (aldex, RRID:SCR_005110)

URL: http://code.google.com/p/aldex/

Resource Type: Resource, software resource

RNA-seq tool that uses the Dirichlet distribution and a transformation to identify genes that exhibit small within-condition and large between-condition variance.

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    AliView

Cite this (AliView, RRID:SCR_002780)

URL: https://github.com/AliView

Resource Type: Resource, software resource

Software for aligning viewing and editing dna / aminiacid sequences, intuitive, fast and leightweight. It has been designed to meet the requirements of next generation sequencing era phylogenetic datasets.

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    Anno-J

Cite this (Anno-J, RRID:SCR_008192)

URL: http://www.annoj.org/

Resource Type: Resource, web service, software resource, data access protocol, source code

A REST-based web application designed for visualizing deep sequencing data and other genome annotation data.

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Cite this (Annotation Ontology, RRID:SCR_002862)

URL: http://code.google.com/p/annotation-ontology/

Resource Type: Resource, ontology, data or information resource, controlled vocabulary

A vocabulary for performing several types of annotation - comment, entities annotation (or semantic tags), textual annotation (classic tags), notes, examples, erratum... - on any kind of electronic document (text, images, audio, tables...) and document parts. AO is not providing any domain ontology but it is fostering the reuse of the existing ones for not breaking the principle of scalability of the Semantic Web.

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Cite this (Antarctic and Southern Ocean Data Portal, RRID:SCR_002193)

URL: http://www.marine-geo.org/portals/antarctic/

Resource Type: Resource, data access protocol, database, web service, service resource, storage service resource, software resource, data repository, data or information resource

Accepts and provides access to geoscience data, primarily marine, collected from oceanographic expeditions in the Antarctic region. The synthesis began in 2003 as the Antarctic Multibeam Bathymetry and Geophysical Data Synthesis (AMBS) with a focus on multibeam bathymetry field data and other geophysical data from the Southern Ocean collected with the R/V N. B. Palmer. In 2005, the effort was expanded to include all routine underway geophysical and oceanographic data collected with both the R/V N. B. Palmer and R/V L. Gould, the two primary research vessels serving the US Antarctic Program. Data available include seafloor bathymetry, subbottom profiling, trackline gravity and magnetics, meteorological, and water column data as well as basic cruise information for all Palmer and Gould expeditions. Seafloor bathymetry data are provided both as raw swath data as well as in gridded form through the Global Multi-Resolution Topography (GMRT) synthesis. This gridded compilation of seafloor bathymetry data can be accessed through GeoMapApp, Create Maps and Grids and through an OGC-compliant Web Map Service. GeoMapApp is an integrated mapping application that provides access to many additional regional bathymetric grids, seismic, radar, gravity and magnetics profiles as well as other map and grid compilations for the Antarctic continent including LIMA.

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Cite this (ArtificialFastqGenerator, RRID:SCR_006880)

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

Resource Type: Resource, software resource

Software that takes the reference genome (in FASTA format) as input and outputs artificial FASTQ files in the Sanger format. It can accept Phred base quality scores from existing FASTQ files, and use them to simulate sequencing errors. Since the artificial FASTQs are derived from the reference genome, the reference genome provides a gold-standard for calling variants (Single Nucleotide Polymorphisms (SNPs) and insertions and deletions (indels)). This enables evaluation of a Next Generation Sequencing (NGS) analysis pipeline which aligns reads to the reference genome and then calls the variants.

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Cite this (AutoPrime, RRID:SCR_000097)

URL: http://www.autoprime.de/AutoPrimeWeb

Resource Type: Resource, analysis service resource, data analysis service, service resource, production service resource

Server to rapidly design primers for real-time PCR measurement of eukaryotic expression.

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    Baa.pl

Cite this (Baa.pl, RRID:SCR_001197)

URL: http://josephryan.github.io/baa.pl/

Resource Type: Resource, software resource

Software tool to evaluate de novo genome assemblies with RNA transcripts.

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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

  • From Current Category

Cite this (BACContigEditor, RRID:SCR_001617)

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

Resource Type: Resource, software resource

A simple sequence alignment editing tool, written in Java.

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    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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    BASE

Cite this (BASE, RRID:SCR_010937)

URL: http://base.thep.lu.se/

Resource Type: Resource, software resource

A comprehensive management application for information, data, and analysis of microarray experiments, available as free open source software.

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Cite this (Basic4Cseq, RRID:SCR_002836)

URL: http://www.bioconductor.org/packages/release/bioc/html/Basic4Cseq.html

Resource Type: Resource, software resource

An R/Bioconductor package for basic filtering, analysis and subsequent near-cis visualization of 4C-seq data. Virtual fragment libraries can be created for any BSGenome package, and filter functions for both reads and fragments and basic quality controls are included. Fragment data in the vicinity of the experiment's viewpoint can be visualized as a coverage plot based on a running median approach and a multi-scale contact profile.

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    BEDOPS

Cite this (BEDOPS, RRID:SCR_012865)

URL: https://github.com/bedops/bedops

Resource Type: Resource, software resource

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

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    BHC

Cite this (BHC, RRID:SCR_006399)

URL: http://master.bioconductor.org/packages/2.13/bioc/html/BHC.html

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

Software package that performs bottom-up hierarchical clustering, using a Dirichlet Process (infinite mixture) to model uncertainty in the data and Bayesian model selection to decide at each step which clusters to merge. This avoids several limitations of traditional methods, for example how many clusters there should be and how to choose a principled distance metric. This implementation accepts multinomial (i.e. discrete, with 2+ categories) or time-series data and also includes a randomised algorithm which is more efficient for larger data sets.

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