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ChopStitch: exon annotation and splice graph construction using transcriptome assembly and whole...
By Rahul Nayak 3017 days agogithub.com - ChopStitch is a new method for finding putative exons and constructing splice graphs using an assembled transcriptome and whole genome shotgun sequencing (WGSS) data. ChopStitch identifies exon-exon boundaries in de novo assembled RNA-seq data with...Collection of Graph Visualization tools !
By Neel 1350 days agopangenome.github.io - Standard approaches to genome inference and analysis relate sequences to a single linear reference genome. This is efficient but has a fundamental problem: Differences from this reference are hard to observe and describe in a coherent way. Variation...PG2: Making Pangenome Graphs Easier to Understand
By Jitendra Narayan 49 days agoGenomics is moving beyond the traditional approach of studying DNA using a single reference genome. Today, researchers are increasingly using pangenomes, which represent genetic information from multiple genomes and capture a much broader range of...d3Network:Tools for creating D3 JavaScript network, tree, dendrogram, and Sankey graphs from R.
By Jit 3105 days agochristophergandrud.github.io - Mike Bostock’s D3.js is great for creating interactive network graphs with JavaScript. The d3Network package makes it easy to create these network graphs from R. The main idea is that you should able to take...GMOL: An Interactive Tool for 3D Genome Structure Visualization
By Jit 3121 days agowww.nature.com - GMOL was developed based upon our multi-scale approach that allows a user to scale between six separate levels within the genome. With GMOL, a user can choose any unit at any scale and scale it up or down to visualize its structure and retrieve...GLEAN: an unsupervised learning system to integrate disparate sources of gene structure evidence
By Poonam Mahapatra 3048 days agosourceforge.net - GLEAN is an unsupervised learning system to integrate disparate sources of gene structure evidence (gene model predictions, EST/protein genomic sequence alignments, SAGE/peptide tags, etc) to produce a consensus gene prediction, without prior...Caretta – A multiple protein structure alignment and feature extraction suite
By Rahul Nayak 2118 days agowww.bioinformatics.nl - Caretta – a multiple protein structure alignment and feature extraction suite Caretta, a multiple structure alignment suite meant for homologous but sequentially divergent protein families which consistently returns accurate alignments...SvABA: Structural variation and indel detection by local assembly
By Jit 2401 days agogithub.com - SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li....Maq: Mapping and Assembly with Quality
By Jit 3605 days agomaq.sourceforge.net - Maq stands for Mapping and Assembly with Quality It builds assembly by mapping short reads to reference sequences. Maq is a project hosted by SourceForge.net. The project page is available athttp://sourceforge.net/projects/maq/....R Graphs !!
By Jit 3623 days ago Comments (1)rgraphgallery.blogspot.be - The blog is a collection of script examples with example data and output plots. R produce excellent quality graphs for data analysis, science and business presentation, publications and other purposes. Self-help codes and examples are provided....
