Jit
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GLEAN: an unsupervised learning system to integrate disparate sources of gene structure evidence
By Poonam Mahapatra 2365 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...GeNeCK (Gene Network Construction Kit) is a comprehensive online tool kit that integrate various...
By Rahul Nayak 2138 days agolce.biohpc.swmed.edu - GeNeCK (Gene Network Construction Kit) is a comprehensive online tool kit that integrate various statistical methods to construct gene networks based on gene expression data and optional hub gene information. It efficiently constructs gene...MAGIC: A tool for predicting transcription factors and cofactors driving gene sets using ENCODE data
By BioStar 1457 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...GeneProf: analysis of high-throughput sequencing experiment
By Jit 2697 days agowww.geneprof.org - GeneProf is a web-based, graphical software suite that allows users to analyse data produced using high-throughput sequencing platforms (RNA-seq and ChIP-seq; "Next-Generation Sequencing" or NGS): Next-gen analysis for next-gen data! Some of...CSA: A high-throughput chromosome-scale assembly pipeline for vertebrate genomes
By Jit 1353 days agogithub.com - The pipeline can use information from scaffolded assemblies (for example from HiC or 10X Genomics), or even from diverged (~65-100 Mya) reference genomes for ordering the contigs and thus support the assembly process. This typically results in...VESPA: Very large-scale Evolutionary and Selective Pressure Analyses
By Jit 1980 days agogithub.com - find the resources we provide here useful in getting you set up to analyse and interpret your data. To reference VESPA: https://peerj.com/preprints/1895/ Documentation is now hosted on ReadTheDocsPIT Bioinformatics Group
PIT Bioinformatics Group solves problems in bioinformatics and computational biology. Recent developed online tools: - Budapest Reference Connectome: View a parametrizable connectome (brain graph). - AmphoraNet: The webserver implementation of...sunbeam: A robust, extensible metagenomics pipeline
By Jit 1618 days agogithub.com - Sunbeam is a pipeline written in snakemake that simplifies and automates many of the steps in metagenomic sequencing analysis. It uses conda to manage dependencies, so it doesn't have pre-existing dependencies or admin...Lorikeet: Strain resolver for metagenomics
By BioStar 139 days agogithub.com - Lorikeet is a within-species variant analysis pipeline for metagenomic communities that utilizes both long and short reads. Lorikeet utilizes a re-implementaion of the GATK HaplotypeCaller algorithm, performing local re-assembly of potentially...Bambus
By Jit 3020 days agowww.cbcb.umd.edu - Bambus 2.0, the second generation Bambus scaffolder available as an open source package. While most other scaffolders are closely tied to a specific assembly program, Bambus accepts the output from most current assemblers and provides the user with...
