Jit
Enthusiast computational biologist with business dream !!!
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mixtureS: a novel tool for bacterial strain reconstruction from reads
By BioStar 2114 days agowww.cs.ucf.edu - mixtureS that can de novo identify bacterial strains from shotgun reads of a clonal or metagenomic sample, without prior knowledge about the strains and their variations. Tested on 243 simulated datasets and 195 experimental datasets, mixtureS...MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
By BioStar 2017 days agogithub.com - The algorithm presented herein, Mining Algorithm for GenetIc Controllers (MAGIC), uses ENCODE ChIP-seq data to look for statistical enrichment of TFs and cofactors in gene bodies and flanking regions in gene lists without...Comparative genomics visualisation tools !
By Neel 1569 days agocmdcolin.github.io - Comparative genomics visualisation tools !Alvis: a tool for contig and read ALignment VISualisation and chimera detection
By LEGE 758 days agogithub.com - Alvis, a simple command line tool that can generate visualisations for a number of common alignment analysis tasks. Alvis is a fast and portable tool that accepts input in a variety of alignment formats and will output production ready vector...NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic...
By LEGE 633 days agogithub.com - NGenomeSyn: an easy-to-use and flexible tool for publication-ready visualization of syntenic relationships across multiple genomes NGenomeSyn [multiple (N) Genome Synteny], for publication-ready visualization of syntenic relationships of...You and your friend have similar DNA !!!
By Jit 4330 days agoYour friends may be as genetically similar to you as your fourth cousin ...Best Practices for Variant Calling with the GATK
By biogeek 2295 days agowww.broadinstitute.org - The presentations below were filmed during the March 2015 GATK Workshop, part of the BroadE Workshop series. At the time of this workshop, the current version of Broad’s Genome Analysis Toolkit (GATK) was version...Variant Calling Resequencing-Based Genome Inference
By Abhi 674 days agoevomics.org - Variant Calling - Resequencing-Based Genome Inference Erik GarrisonUniversity of Tennessee Health Science CenterWorkshop on Genomics - Český KrumlovJanuary 12,...vcfR: a package to manipulate and visualize VCF data in R
By Jit 2780 days agogithub.com - VcfR is an R package intended to allow easy manipulation and visualization of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices from...LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data
By BioStar 2299 days agocsb5.github.io - LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or...
