Upalabdha's repositories
appliedgenomics2021
Materials for Spring 2021 Applied Genomics Course
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.
variant-calling-pipeline-gatk4
Variant Calling Pipeline Using GATK4 and Nextflow
orthologcollector
Parses a reference genome for orthologs of a protein
DupGen_finder
A pipeline used to identify different modes of duplicated gene pairs
AA_Comp
Evolutionary changes in aa composition of orthlogous genes during vertebrate evolution
genome-scripts
Genome Scripts used in fungal comparative genomics
microbial-informatics-2014
Microbial Whole Genome Sequence data analysis labs for 2014
BADAS_Nextflow_Tutorial
Nextflow tutorial for the BADAS series at NYU Center for Genomics and Systems Biology
FunFinder_Pangenome
Data analysis of Funannotate and Orthofinder outputs to Pangenome results
Microbial-bioinformatics-introductory-course-Material-2018
Course material for OPEN & REPRODUCIBLE MICROBIOME DATA ANALYSIS SPRING SCHOOL
M3C
Monte Carlo Reference-based Consensus Clustering
collinearity
scripts to parse and analyse MCScanX collinearity output
ena-dl
Download FASTQ files from ENA
Latex_templates
a collection of useful templates for working across projects
bac-genomics-scripts
Collection of scripts for bacterial genomics
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
appliedgenomics2018
Materials for Spring 2018 Applied Genomics Course
bioinf529-winter2019
Bioinformatics 529 - Bioinformatics Concepts and Algorithms
bi028
Course materials for "Linux programming for Bioinformatics"
bioinformatics
Course materials for Computational Biology and Bioinformatics - BI462
elearningcollection
A collection of random and not so random online learning materials for biology, computation, and bioinformatics
DNAflexsuite
A suite of tools to predict DNA flexibility from sequence at different resolutions
bioinformatics-tools
Awk, bash, python scripts for processing NGS data
Genomic-Data-Science
Genomic data science specialization
paper-zhang2014_whole_genome_alignments
Source code from Zhang et al., (2014) Genomic data of avian phylogenomics project. GigaScience 3:26