Rahul Agarwal
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Parliament2: Runs a combination of tools to generate structural variant calls on whole-genome...
By Jit 1618 days agogithub.com - Parliament2 identifies structural variants in a given sample relative to a reference genome. These structural variants cover large deletion events that are called as Deletions of a region, Insertions of a sequence into a region, Duplications of a...Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
By Neel 980 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 +...UCSC SARS-CoV-2 Genome Browser
By Jit 1030 days agowww.nature.com - The UCSC SARS-CoV-2 Genome Browser (https://genome.ucsc.edu/covid19.html) is an adaptation of our popular genome-browser visualization tool for this virus, containing many annotation tracks and new features, including conservation with similar...Calling narrow and broad peaks from ChIP-Seq data
By Strand 3377 days agoCalling narrow and broad peaks from ChIP-Seq dataMIT Computational Biology Group
My research group consists primarily of computer science graduate students and postdocs with expertise in algorithms, statistical inferences and machine learning, and sharing a passion for understanding fundamental biological problems. We work in...Bioinformatics PhD studentship available in New Zealand
Bioinformatics PhD studentship available in New Zealand The importance of transcriptional control has been explored in a burgeoning line of research over several decades; nevertheless, we are still far from having a complete picture of the...RNA-Seq De novo Assembly Using Trinity
By Surabhi Chaudhary 3145 days agogithub.com - Trinity, developed at the Broad Institute and the Hebrew University of Jerusalem, represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-seq data. Trinity combines three independent software modules:...NCBI Magic-BLAST
By Jit 2271 days agoncbi.github.io - Magic-BLAST is a tool for mapping large next-generation RNA or DNA sequencing runs against a whole genome or transcriptome. Each alignment optimizes a composite score, taking into account simultaneously the two reads of a pair, and in case of...LncPipe:A Nextflow-based pipeline for comprehensive analyses of long non-coding RNAs from RNA-seq...
By LEGE 1142 days agogithub.com - The pipeline was developed based on a popular workflow framework Nextflow, composed of four core procedures including reads alignment, assembly, identification and quantification. It contains various unique features such as well-designed...deepTools
By Martin Jones 3646 days agoUser-friendly tools for the normalization and visualization of deep-sequencing data
