Shruti Paniwala
A Bioinformatician
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MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
By BioStar 2017 days agogithub.com - The algorithm presented herein, Mining Algorithm for GenetIc Controllers (MAGIC), uses ENCODE ChIP-seq data to look for statistical enrichment of TFs and cofactors in gene bodies and flanking regions in gene lists without...R package for visualising GO enrichment
By Jit 4701 days agoR package for visualising GO enrichment results as wordclouds is available at CRANclusterProfiler
By Jit 3641 days agowww.bioconductor.org - statistical analysis and visulization of functional profiles for genes and gene clustersBioconductor version: Release (3.3)This package implements methods to analyze and visualize functional profiles (GO and KEGG) of gene and gene clusters.Author:...
Pathway Analysis
Last updated 4257 days ago by Rahul Agarwal Comments (2)Pathway Analysis is usually performed with aim to enrich the genes with their functional information and reveal the underlying biological mechanisms pursue by genes. Pathway Analysis is not only limited to what biological pathways a particular set...RaGOO: Fast Reference-Guided Scaffolding of Genome Assembly Contigs
By Jit 2414 days agogithub.com - Alonge M, Soyk S, Ramakrishnan S, Wang X, Goodwin S, Sedlazeck FJ, Lippman ZB, Schatz MC: Fast and accurate reference-guided scaffolding of draft genomes. bioRxiv 2019. RaGOO is a tool for coalescing genome assembly contigs into...HECIL: A Hybrid Error Correction Algorithm for Long Reads with Iterative Learning
By Abhimanyu Singh 2712 days agogithub.com - HECIL—Hybrid Error Correction with Iterative Learning—a hybrid error correction framework that determines a correction policy for erroneous long reads, based on optimal combinations of decision weights obtained from short read...Janggu - Deep learning for Genomics
By Jit 1901 days agogithub.com - Janggu is a python package that facilitates deep learning in the context of genomics. The package is freely available under a GPL-3.0 license. Detail tutorial at https://janggu.readthedocs.io/en/latest/ USE...LAST
By Bulbul 3455 days agohttp://last.cbrc.jp/ - LAST can: Handle big sequence data, e.g: Compare two vertebrate genomes Align billions of DNA reads to a genome Indicate the reliability of each aligned column. Use sequence quality data properly. Compare DNA...PLAST: A fast, accurate and NGS scalable bank-to-bank sequence similarity search tool
By Jit 3109 days agohttps://plast.inria.fr/ - PLAST is a fast, accurate and NGS scalable bank-to-bank sequence similarity search tool providing significant accelerations of seeds-based heuristic comparison methods, such as the Blast suite of algorithms. Relying on unique software architecture,...
