CRAVAT 4.0 – Cancer-related Analysis of Variants Toolkit

 Genetics & Pedigree 179 views Comments Off on CRAVAT 4.0 – Cancer-related Analysis of Variants Toolkit
May 042016
 

CRAVAT 4.0

:: DESCRIPTION

CRAVAT is a web server with simple interface where cancer-related analysis of variants are performed.CRAVAT currently employs three analysis tools, CHASM, SNVGet, and VEST.

::DEVELOPER

Karchin Lab

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

CRAVAT: cancer-related analysis of variants toolkit.
Douville C, Carter H, Kim R, Niknafs N, Diekhans M, Stenson PD, Cooper DN, Ryan M, Karchin R.
Bioinformatics. 2013 Mar 1;29(5):647-8. doi: 10.1093/bioinformatics/btt017. Epub 2013 Jan 16.

gffcompare 0.9.6f – Comparing, Annotating, Merging and Tracking Transcripts in GFF files

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May 042016
 
gffcompare 0.9.6f - Comparing, Annotating, Merging and Tracking Transcripts in GFF files

gffcompare 0.9.6f :: DESCRIPTION gffcompare is a program for comparing, annotating, merging and tracking transcripts in GFF(General Feature Format) files ::DEVELOPER The Center for Computational Biology at Johns Hopkins University :: SCREENSHOTS N/A :: REQUIREMENTS Linux / Mac OsX :: DOWNLOAD  gffcompare :: MORE INFORMATION

gffread 0.94f – Filtering, Converting and Manipulating GFF files

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May 042016
 
gffread 0.94f - Filtering, Converting and Manipulating GFF files

gffread 0.94f :: DESCRIPTION The program gffread can be used to validate, filter, convert and perform various other operations on GFF (General Feature Format) files. ::DEVELOPER The Center for Computational Biology at Johns Hopkins University :: SCREENSHOTS N/A :: REQUIREMENTS Linux / Mac OsX :: DOWNLOAD  gffread :: MORE INFORMATION

fqtrim 0.95 – Trimming & Filtering of Next-gen Reads

 DNA / Genome Analysis 188 views Comments Off on fqtrim 0.95 – Trimming & Filtering of Next-gen Reads
May 042016
 
fqtrim 0.95 - Trimming & Filtering of Next-gen Reads

fqtrim 0.95 :: DESCRIPTION fqtrim is a software utility for filtering and trimming high-throughput next-gen reads. ::DEVELOPER Center for Computational Biology , Johns Hopkins University School of Medicine :: SCREENSHOTS N/A :: REQUIREMENTS Linux :: DOWNLOAD   fqtrim :: MORE INFORMATION

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May 042016
 
DupLoCut - Duplication Loss Phylogeny by Cutting Planes

DupLoCut :: DESCRIPTION DupLoCut computes ancestral gene orders, given a phylogenetic tree and gene orders assigned to the leaves of the tree. It attempts to find the most parsimony assignment of gene orders under the duplication-loss evolutionary model. ::DEVELOPER The Center for Computational Biology at Johns Hopkins University :: SCREENSHOTS N/A :: REQUIREMENTS Linux / […]

Centrifuge 1.0.1-beta – Classifier for Metagenomic Sequences

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May 042016
 
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Centrifuge 1.0.1-beta :: DESCRIPTION Centrifuge is a very rapid and memory-efficient system for the classification of DNA sequences from microbial samples, with better sensitivity than and comparable accuracy to other leading systems. ::DEVELOPER The Center for Computational Biology at Johns Hopkins University :: SCREENSHOTS N/A :: REQUIREMENTS Linux / Mac OsX :: DOWNLOAD  Centrifuge :: MORE […]

Kraken 0.10.5-beta – Kraken Taxonomic Sequence Classification System

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May 042016
 
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Kraken 0.10.5-beta :: DESCRIPTION Kraken is a very fast system for taxonomic classification of short or long DNA sequences from a microbiome or metagenomic sample. ::DEVELOPER The Center for Computational Biology at Johns Hopkins University :: SCREENSHOTS N/A :: REQUIREMENTS Linux / Mac OsX :: DOWNLOAD  Kraken :: MORE INFORMATION Citation Genome Biol. 2014 Mar 3;15(3):R46. […]

Diamund – DIrect Alignment for MUtatioN Discovery

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May 042016
 
Diamund - DIrect Alignment for MUtatioN Discovery

Diamund :: DESCRIPTION Diamund is a new, efficient algorithm for variant detection that compares DNA sequences directly to one another, without aligning them to the reference genome. ::DEVELOPER The Center for Computational Biology at Johns Hopkins University :: SCREENSHOTS N/A :: REQUIREMENTS Linux / Mac OsX :: DOWNLOAD  Diamund :: MORE INFORMATION Citation Hum Mutat. […]

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May 042016
 
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Ballgown :: DESCRIPTION Ballgown is a software package designed to facilitate flexible differential expression analysis of RNA-Seq data. It also provides functions to organize, visualize, and analyze the expression measurements for your transcriptome assembly. ::DEVELOPER The Center for Computational Biology at Johns Hopkins University :: SCREENSHOTS N/A :: REQUIREMENTS Linux / Mac OsX R/BioCouductor :: […]

HISAT / HISAT2 2.0.3-beta – Hierarchical Indexing for Spliced Alignment of Transcripts

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HISAT / HISAT2 2.0.3-beta - Hierarchical Indexing for Spliced Alignment of Transcripts

HISAT / HISAT2 2.0.3-beta :: DESCRIPTION HISAT is a fast and sensitive spliced alignment program for mapping RNA-seq reads. HISAT2 is a successor to both HISAT and TopHat2. HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single […]