Rahul Nayak
A Bioinformatician
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vt: a variant tool set that discovers short variants from Next Generation Sequencing data.
By Jit 1790 days agogenome.sph.umich.edu - vt is a variant tool set that discovers short variants from Next Generation Sequencing data. https://genome.sph.umich.edu/wiki/Vt https://github.com/atks/vtJuicebox: Visualization and analysis software for Hi-C data
By Jit 1767 days agogithub.com - Juicebox is visualization software for Hi-C data. This distribution includes the source code for Juicebox, Juicer Tools, and Assembly Tools. Download Juicebox here, or use Juicebox on the web. Detailed documentation is...Useful links to therapy, disease, drug and drug-target network data:
By Jit 1665 days agoUseful resources to therapy, disease, drug and drug-target network dataMAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
By BioStar 1487 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...LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data
By Neel 1278 days ago Comments (1)academic.oup.com - LoReTTA (Long Read Template-Targeted Assembler), a tool designed for performing de novo assembly of long reads generated from viral genomes on the PacBio platform. LoReTTA exploits a reference genome to guide the assembly process, an approach that...Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
By Neel 1031 days agogithub.com - This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA +...OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes
By Abhi 601 days agoorthovenn3.bioinfotoolkits.net - OrthoVenn3 is a powerful tool for comparative genomics analysis, used as a web server for full genome comparisons, annotation, and evolutionary analysis of orthologous clusters across multiple species. It has already been used by thousands of users...
Import R Data
Last updated 2720 days ago by Abhimanyu SinghIt is often necessary to import sample textbook data into R before you start working on your homework. Excel File Quite frequently, the sample data is in Excel format, and needs to be imported into R prior to use. For this, we can...NCBI to assist in Virus Hunting Data Science Hackathon
By BioStar 2229 days agoNCBI Hackathon are pleased to announce the second installment of the SoCal Bioinformatics Hackathon. From January 9-11, 2019, the NCBI will help run a bioinformatics hackathon in Southern California hosted by the Computational Sciences Research...De novo Genome Assembly for Illumina Data
By Rahul Nayak 1798 days agowww.melbournebioinformatics.org.au - Written and maintained by Simon Gladman - Melbourne Bioinformatics (formerly VLSCI) Protocol Overview / Introduction In this protocol we discuss and outline the process of de novo assembly for small to medium sized...
