Jit
Enthusiast computational biologist with business dream !!!
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PureCN: copy number calling and SNV classification using targeted short read sequencing
By Jit 2866 days agobioconductor.org - This package estimates tumor purity, copy number, and loss of heterozygosity (LOH), and classifies single nucleotide variants (SNVs) by somatic status and clonality. PureCN is designed for targeted short read sequencing data, integrates well with...URMAP, an ultra-fast read mapper
By Jit 2053 days ago Comments (1)github.com - URMAP, a new read mapping algorithm. URMAP is an order of magnitude faster than BWA with comparable accuracy on several validation tests. On a Genome in a Bottle (GIAB) variant calling test with 30× coverage 2×150 reads, URMAP achieves...List of popular bioinformatics software/tools
By Jitendra Narayan 4715 days ago Comments (28)samtools.sourceforge.net - In current genome era, our day to day work is to handle the huge geneome sequences, expression data, several other datasets. This link provide a comprehensive list of commonly used sofware/tools.deepTools
By Martin Jones 4235 days agoUser-friendly tools for the normalization and visualization of deep-sequencing dataComputer simulation of genetic mechanism !!
By Jit 3744 days ago Comments (2)Computer simulation is the discipline of designing a model of an actual or theoretical physical/biological system, executing the model on a digital computer, and analyzing the execution output.
Tools for Searching Repeats And Palindromic Sequences
Last updated 2981 days ago by Poonam Mahapatra Comments (2)What are genomic interspersed repeats? In the mid 1960's scientists discovered that many genomes contain stretches of highly repetitive DNA sequences ( see Reassociation Kinetics Experiments, and C-Value Paradox ). These sequences were later...CSBB-v1.0
By Neel 3636 days agogithub.com - CSBB is a command line based bioinformatics suite to analyze biological data acquired through varied avenues of biological experiments. CSBB is implemented in Perl, while it also leverages the use of R and python in background for specific modules....Finding Patterns in Biological Sequences
By Jit 3460 days agoengr.case.edu - In this report we provide an overview of known techniques for discovery of patterns of biological sequences (DNA and proteins). We also provide biological motivation, and methods of biological verification of such patterns. Finally we list publicly...WGS Celera Assembler version 8.3rc2
By Jit 3352 days agowgs-assembler.sourceforge.net - These are release notes for Celera Assembler version 8.3rc2, which was released on May 24, 2015.This distribution package provides a stable, tested, documented version of the software. The distribution is usable on most Unix-like platforms,...-
Tools to Predict the Impact of Missense Variants !
Last updated 2973 days ago by JitPrioritizing missense variants for further experimental investigation is a key challenge in current sequencing studies for exploring complex and Mendelian diseases. A large number of in silico tools have been employed for the task of...
