Jit
Enthusiast computational biologist with business dream !!!
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Modular, efficient and constant-memory single-cell RNA-seq preprocessing
By Jit 1800 days ago Comments (1)pachterlab.github.io - With kallisto | bustools you can Generate a cell x gene or cell x transcript equivalence class count matrix Perform RNA velocity and single-nuclei RNA-seq analsis Quantify data from numerous technologies such as...proActiv: Estimation of Promoter Activity from RNA-Seq data
By BioStar 2035 days agogithub.com - proActiv is an R package that estimates promoter activity from RNA-Seq data. proActiv uses aligned reads and genome annotations as input, and provides absolute and relative promoter activity as output. The package can be used to identify active...BioJupies: Automatically Generates RNA-seq Data Analysis Notebooks
By Rahul Nayak 1906 days agoamp.pharm.mssm.edu - With BioJupies you can produce in seconds a customized, reusable, and interactive report from your own raw or processed RNA-seq data through a simple user interface BioJupies now supports user accounts! Sign in from the top right corner of the page...Kallisto vs Salmon: Choosing the Right Tool for RNA-Seq Quantification
By BioStar 312 days agoIn the world of transcriptomics, quantifying gene and transcript expression accurately and efficiently is crucial. With the explosion of RNA-Seq data, researchers have turned to fast, alignment-free tools that streamline the quantification process...karyoploteR: plot whole genomes with arbitrary data
By Abhimanyu Singh 2958 days agobernatgel.github.io - karyoploteR is an R package to create karyoplots, that is, representations of whole genomes with arbitrary data plotted on them. It is inspired by the R base graphics system and does not depend on other graphics packages. The aim of karyoploteR...Scripts for the analysis of HGT in genome sequence data.
By Jit 3022 days agogithub.com - Scripts for the analysis of HGT in genome sequence dataHeap: a highly sensitive and accurate SNP detection tool for low-coverage high-throughput...
By Jit 2882 days agogithub.com - Heap, that enables robustly sensitive and accurate calling of SNPs, particularly with a low coverage NGS data, which must be aligned to the reference genome sequences in advance. To reduce false positive SNPs, Heap determines genotypes and calls...Epiviz: an interactive visualization tool for functional genomics data.
By Jit 2801 days agohttps://epiviz.github.io/ - Epiviz is an interactive visualization tool for functional genomics data. It supports genome navigation like other genome browsers, but allows multiple visualizations of data within genomic regions using scatterplots, heatmaps and other...VariantBam: Filtering and profiling of next-generational sequencing data using region-specific rules
By Rahul Nayak 2713 days agogithub.com - VariantBam is a tool to extract/count specific sets of sequencing reads from next-generational sequencing files. To save money, disk space and I/O, one may not want to store an entire BAM on disk. In many cases, it would be more efficient to store...EXCAVATOR: detecting copy number variants from whole-exome sequencing data
By Radha Agarkar 2622 days agosourceforge.net - EXCAVATOR, for the detection of copy number variants (CNVs) from whole-exome sequencing data. EXCAVATOR combines a three-step normalization procedure with a novel heterogeneous hidden Markov model algorithm and a calling method that classifies...
