Shruti Paniwala
A Bioinformatician
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Gene Ontology Consortium
By Jit 2764 days agowww.geneontology.org - The GO knowledgebase is composed of two primary components: the Gene Ontology (GO), which provides the logical structure of the biological functions (‘terms’) and their relationships to one another, manifested as a directed...A guide to machine learning for biologists
By Abhi 1683 days agowww.nature.com - Because of the increasing size and inherent complexity of biological data, there has been an increase in the application of machine learning in biology to create useful and predictive models of the underlying biological processes. All machine...modelStudio: a package automates the explanation of machine learning predictive models
By Jit 2388 days agomodeloriented.github.io - The modelStudio package automates the explanation of machine learning predictive models. This package generates advanced interactive and animated model explanations in the form of a serverless HTML site. It...REVIGO: Reduced Visualize gene ontology
By Jit 2929 days agohttp://revigo.irb.hr/ - REViGO can take long lists of Gene Ontology terms and summarize them by removing redundant GO terms. The remaining terms can be visualized in semantic similarity-based scatterplots, interactive graphs, or tag clouds. More about...GLEAN: an unsupervised learning system to integrate disparate sources of gene structure evidence
By Poonam Mahapatra 2987 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...A guide to machine learning for biologists
By LEGE 1786 days agowww.nature.com - We aim to provide readers with a gentle introduction to a few key machine learning techniques, including the most recently developed and widely used techniques involving deep neural networks. We describe how different techniques may be suited to...PASA: Gene Structure Annotation and Analysis
By biogeek 3145 days agopasapipeline.github.io - PASA, acronym for Program to Assemble Spliced Alignments, is a eukaryotic genome annotation tool that exploits spliced alignments of expressed transcript sequences to automatically model gene structures, and to maintain gene structure annotation...MetaEuk - sensitive, high-throughput gene discovery and annotation for large-scale eukaryotic...
By Jit 2031 days agogithub.com - MetaEuk is a modular toolkit designed for large-scale gene discovery and annotation in eukaryotic metagenomic contigs. Metaeuk combines the fast and sensitive homology search capabilities of MMseqs2 with a dynamic programming procedure to...AlignGraph: algorithm for secondary de novo genome assembly guided by closely related references
By Manisha Mishra 3033 days agogithub.com - AlignGraph is a software that extends and joins contigs or scaffolds by reassembling them with help provided by a reference genome of a closely related organism. Using AlignGraph AlignGraph --read1 reads_1.fa --read2 reads_2.fa --contig contigs.fa...A Brief Bioinformatics Tutorial
By Jit 4460 days ago Comments (4)www.mrc-lmb.cam.ac.uk - This is about how to use a computer to find what is known about a gene of interest and also how to get new insights about it. The tutorial is divided in three main parts: In the Sequence part, you will see how to look efficiently for a...
