Radha Agarkar
A Bioinformatician
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ReConPlot: an R package for the visualization and interpretation of genomic rearrangements
By LEGE 347 days agoacademic.oup.com - ReConPlot (REarrangement and COpy Number PLOT), an R package that provides functionalities for the joint visualization of SCNAs and SVs across one or multiple chromosomes. ReConPlot is based on the popular ggplot2 package, thus allowing...GPOPSIM: a simulation tool for whole-genome genetic data
By Jit 2504 days agogithub.com - GPOPSIM is a simulation tool for pedigree, phenotypes, and genomic data, with a variety of population and genome structures and trait genetic architectures. It provides flexible parameter settings for a wide discipline of users, especially can...BFC: a standalone high-performance tool for correcting sequencing errors from Illumina sequencing...
By Jit 2370 days agogithub.com - BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes. The BFC algorithm is a...NanoPack: visualizing and processing long-read sequencing data
By Jit 2298 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 2167 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 2149 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 1780 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...vt: a variant tool set that discovers short variants from Next Generation Sequencing data.
By Jit 1763 days agogenome.sph.umich.edu - vt is a variant tool set that discovers short variants from Next Generation Sequencing data. https://genome.sph.umich.edu/wiki/Vt https://github.com/atks/vtJuicebox: Visualization and analysis software for Hi-C data
By Jit 1739 days agogithub.com - Juicebox is visualization software for Hi-C data. This distribution includes the source code for Juicebox, Juicer Tools, and Assembly Tools. Download Juicebox here, or use Juicebox on the web. Detailed documentation is...Useful links to therapy, disease, drug and drug-target network data:
By Jit 1638 days agoUseful resources to therapy, disease, drug and drug-target network data
