Shruti Paniwala
A Bioinformatician
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NanoPack: visualizing and processing long-read sequencing data
By Jit 2297 days agogithub.com - The NanoPack tools are written in Python3 and released under the GNU GPL3.0 License. The source code can be found at https://github.com/wdecoster/nanopack, together with links to separate scripts and their documentation. The scripts are...ALLHiC: Phasing and scaffolding polyploid genomes based on Hi-C data
By BioStar 2165 days agogithub.com - The major problem of scaffolding polyploid genome is that Hi-C signals are frequently detected between allelic haplotypes and any existing stat of art Hi-C scaffolding program links the allelic haplotypes together. To solve the problem, we developed...kallisto: a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data
By Jit 2147 days ago Comments (1)pachterlab.github.io - kallisto is a program for quantifying abundances of transcripts from bulk and single-cell RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. It is based on the novel idea of pseudoalignment for...heatmaply: popular graphical method for visualizing high-dimensional data
By Neel 1778 days agotalgalili.github.io - This work is based on ggplot2 and plotly.js engine. It produces similar heatmaps as d3heatmap, with the advantage of speed (plotly.js is able to handle larger size matrix), and the ability to zoom from the dendrogram. heatmaply also provides an...Phytozome v12.1: plant science community hub for accessing palnts genomic data
By Surabhi Chaudhary 1712 days agophytozome.jgi.doe.gov - Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, provides JGI users and the broader plant science community a hub for accessing, visualizing and analyzing JGI-sequenced plant genomes, as well as...proActiv: Estimation of Promoter Activity from RNA-Seq data
By BioStar 1563 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...3D Genome Browser: explore chromatin interaction data, such as Hi-C, ChIA-PET, Capture Hi-C,...
By BioStar 1401 days ago3dgenome.fsm.northwestern.edu - Beside visualizing chromatin interaction data, you can also seamlessly browse other omics data such as ChIP-Seq or RNA-Seq for the same genomic region, and gain a complete view of both regulatory landscape and 3D genome structure for any given gene....Refseq viraal genome sequences !
By Jit 1078 days agoftp.ncbi.nlm.nih.gov - List of all viruses on NCBI https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/Powerful books for learning data analysis with R
By LEGE 179 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 68 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...
