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Troyanskaya Lab
The goal of our research is to interpret and distill this complexity through accurate analysis and modeling of molecular pathways, particularly those in which malfunctions lead to the manifestation of disease. We are inventing integrative methods...
ProteoClade: A taxonomic toolkit for multi-species and metaproteomic analysis
By Jit 1743 days agogithub.com - ProteoClade is a Python library for taxonomic-based annotation and quantification of bottom-up proteomics data. It is designed to be user-friendly, and has been optimized for speed and storage requirements. ProteoClade helps you analyze two...RNA-seq workflow: gene-level exploratory analysis and differential expression
By Jit 1173 days agomaster.bioconductor.org - Here we walk through an end-to-end gene-level RNA-seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were quantified to the reference transcripts, and prepare gene-level count...Tools for Differential expression analysis
By Abhi 778 days ago Comments (1)the sequenced reads can be mapped to the organism’s genes to assess how differently the genes are expressed under the experimental circumstances as opposed to the control scenario. This is known as differential expression (DE) analysisIQ-TREE: Efficient software for phylogenomic inference
By Jit 2137 days agohttp://www.iqtree.org/ - A fast and effective stochastic algorithm to infer phylogenetic trees by maximum likelihood. IQ-TREE compares favorably to RAxML and PhyML in terms of likelihoods with similar computing time IQ-TREE found higher likelihoods between 62.2%...Next generation sequencing(NGS) books
By Abhimanyu Singh 3862 days ago Comments (1)en.wikibooks.org - Employing different technologies, the purpose of NGS platform is to decode the identity or modification on the nucleotides. NGS platforms evolve quickly and capture the main stream. This bookmark is created to provide NGS online books links.RATT
By Jitendra Narayan 3244 days agoratt.sourceforge.net - RATT is software to transfer annotation from a reference (annotated) genome to an unannotated query genome. It was first developed to transfer annotations between different genome assembly versions. However, it can also transfer annotations between...DIAL
By Abhimanyu Singh 2856 days agowww.bx.psu.edu - A computational pipeline for identifying single-base substitutions between two closely related genomes without the help of a reference genome. DIAL works even when the depth of coverage is insufficient for de novo assembly, and it can be extended to...funannotate: Eukaryotic Genome Annotation Pipeline
By Jit 2289 days agogithub.com - Funannotate is a genome prediction, annotation, and comparison software package. It was originally written to annotate fungal genomes (small eukaryotes ~ 30 Mb genomes), but has evolved over time to accomodate larger genomes. The impetus for this...Basic Structure of Snakemake Pipeline Run !
By Abhi 1168 days agoBrief Overview of Snakemake Pipeline Commands
