Pinned Repositories
AA_Comp
Evolutionary changes in aa composition of orthlogous genes during vertebrate evolution
Analyses_Pipelines
Analyses pipelines that I use for my work
ANIclustermap
A tool for drawing ANI clustermap between all-vs-all microbial genomes using fastANI & seaborn
applied-computational-genomics
Applied Computational Genomics Course at UU: Spring 2020
appliedgenomics2018
Materials for Spring 2018 Applied Genomics Course
bioinformatics
Course materials for Computational Biology and Bioinformatics - BI462
gene-expansion
jcvi
Python library to facilitate genome assembly, annotation, and comparative genomics
SequenceTools
Programs used in the lab for various tasks
star_protocols_wes3x
Functional code templates for the Star Protocols paper describing consolidated WES variant calling with 3 callers
UpalabdhaD's Repositories
UpalabdhaD/bioinformatics
Course materials for Computational Biology and Bioinformatics - BI462
UpalabdhaD/AA_Comp
Evolutionary changes in aa composition of orthlogous genes during vertebrate evolution
UpalabdhaD/appliedgenomics2018
Materials for Spring 2018 Applied Genomics Course
UpalabdhaD/appliedgenomics2021
Materials for Spring 2021 Applied Genomics Course
UpalabdhaD/awesome-biology
Curated (meta)list of resources for Biology.
UpalabdhaD/bac-genomics-scripts
Collection of scripts for bacterial genomics
UpalabdhaD/BADAS_Nextflow_Tutorial
Nextflow tutorial for the BADAS series at NYU Center for Genomics and Systems Biology
UpalabdhaD/bash_functions
Functions I keep in my .bash files. Usually written badly by myself (to handle only very specific cases) or also possibly stolen off the internetz
UpalabdhaD/bi028
Course materials for "Linux programming for Bioinformatics"
UpalabdhaD/BiocSwirl
BiocSwirl is a series of in-depth swirlify generated courses used to teach bioinformatics workflows in R/Bioconductor using an interactive and easy to digest format. This project was the People's Choice Award for the Vancouver Bioinformatics Hackathon Hackseq2019.
UpalabdhaD/bioinf529-winter2019
Bioinformatics 529 - Bioinformatics Concepts and Algorithms
UpalabdhaD/bioinformatics-cafe
Unsorted scripts for bioinformatics
UpalabdhaD/bioinformatics-tools
Awk, bash, python scripts for processing NGS data
UpalabdhaD/collinearity
scripts to parse and analyse MCScanX collinearity output
UpalabdhaD/DNAflexsuite
A suite of tools to predict DNA flexibility from sequence at different resolutions
UpalabdhaD/DupGen_finder
A pipeline used to identify different modes of duplicated gene pairs
UpalabdhaD/elearningcollection
A collection of random and not so random online learning materials for biology, computation, and bioinformatics
UpalabdhaD/ena-dl
Download FASTQ files from ENA
UpalabdhaD/FunFinder_Pangenome
Data analysis of Funannotate and Orthofinder outputs to Pangenome results
UpalabdhaD/genome-scripts
Genome Scripts used in fungal comparative genomics
UpalabdhaD/good_background_papers
UpalabdhaD/intro-machine-learning-2018
Course materials for "An Introduction to Machine Learning" (2018)
UpalabdhaD/Latex_templates
a collection of useful templates for working across projects
UpalabdhaD/M3C
Monte Carlo Reference-based Consensus Clustering
UpalabdhaD/Microbial-bioinformatics-introductory-course-Material-2018
Course material for OPEN & REPRODUCIBLE MICROBIOME DATA ANALYSIS SPRING SCHOOL
UpalabdhaD/microbial-informatics-2014
Microbial Whole Genome Sequence data analysis labs for 2014
UpalabdhaD/orthologcollector
Parses a reference genome for orthologs of a protein
UpalabdhaD/pathogen-informatics-training
UpalabdhaD/Sphingomonas-EggNOG-Workbook
Jupyter Notebook for Parsing and comparing annotations using EmapperV2
UpalabdhaD/variant-calling-pipeline-gatk4
Variant Calling Pipeline Using GATK4 and Nextflow