Jit
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ClinCNV: Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data
By Neel 2242 days agogithub.com - ClinCNV detects CNVs in germline and somatic context in NGS data (targeted and whole-genome). We work in cohorts, so it makes sense to try ClinCNV if you have more than 10 samples (recommended amount - 40 since we estimate variances from...LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data
By BioStar 2210 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...Submit your SARS-CoV-2 sequence data to GenBank
By Neel 2158 days agoSubmit your SARS-CoV-2 sequence data to GenBank and SRA with our new submission landing page.McClintock: Meta-pipeline to identify transposable element insertions using next generation...
By BioStar 1958 days agogithub.com - an integrated bioinformatics pipeline for the detection of TE insertions in whole-genome shotgun data, called McClintock (https://github.com/bergmanlab/mcclintock), which automatically runs and standardizes output for multiple TE detection methods....Ktrim: an extra-fast and accurate adapter- and quality-trimmer for sequencing data
By Jit 1850 days agogithub.com - Ktrim is written in C++ for GNU Linux/Unix platforms. After uncompressing the source package, you can find an executable file ktrim under bin/ directory compiled using g++ v4.8.5 and linked with libz...Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
By Neel 1472 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 +...Powerful books for learning data analysis with R
By LEGE 649 days agohttps://r-graphics.org/ - R is powerful tool for data analysis, visualization, and machine learning. And it costs $0 to use! Here are six FREE books you can use to learn R...Figeno: Tool for plotting sequencing data along genomic coordinates.
By LEGE 537 days agogithub.com - Tool for plotting sequencing data along genomic coordinates. FIGENO is a FIGure GENerator for GENOmics With figeno, you can plot various types of sequencing data along genomic coordinates. Video...Managing and Analyzing Next-Generation Sequence Data
By Rahul Agarwal 4320 days agowww.ploscompbiol.org - Centralized Bioinformatics Core Facilities provide shared resources for the computational and IT requirements of the investigators in their department or institution. As such, they must be able to effectively react to new types of experimental...
Import R Data
Last updated 3161 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...
