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/gene-expansion
UpalabdhaD/star_protocols_wes3x
Functional code templates for the Star Protocols paper describing consolidated WES variant calling with 3 callers
UpalabdhaD/Analyses_Pipelines
Analyses pipelines that I use for my work
UpalabdhaD/applied-computational-genomics
Applied Computational Genomics Course at UU: Spring 2020
UpalabdhaD/awesome-courses
:books: List of awesome university courses for learning Computer Science!
UpalabdhaD/awesome-genome-visualization
A list of interesting genome browser or genome-browser-like implementations
UpalabdhaD/awesome-ggplot2
A curated list of awesome ggplot2 tutorials, packages etc.
UpalabdhaD/awesome-sequencing-tech-papers
A collection of publications on comparison of high-throughput sequencing technologies.
UpalabdhaD/bioicons
A library of free open source icons for science illustrations in biology and chemistry
UpalabdhaD/biovcnet.github.io
Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes
UpalabdhaD/CLASS_2021
Statistical and computational analysis of the human genome
UpalabdhaD/Crickets_Genome_Annotation
Gennome annotation scripts for the crickets Gryllus bimaculatus and Laupala kohalensis.
UpalabdhaD/data-science-interview-questions-and-answers
Data science interview questions with answers. Not ideally (yet)
UpalabdhaD/DeepSeqAnalysis
Course materials for a graduate class in applied bioinformatics for biologists
UpalabdhaD/FastANI_heatmap
This repository contains R code for building a heatmap and histogram with the output of FastANI
UpalabdhaD/Gene-Synteny-Analysis
Uses MCscan (python version) to create micro- and macro-synteny plots
UpalabdhaD/genomescope
Fast genome analysis from unassembled short reads
UpalabdhaD/GermlineMutationCalling
An adaptable Snakemake workflow which uses GATKs best practice recommendations to perform germline mutation calling starting with BAM files
UpalabdhaD/HCGS-BASH-tutorial
Getting started on a server
UpalabdhaD/hcoErosions
UpalabdhaD/literature_analysis_pubmed
Part of Pat's Code Club series that started 2022-05-12
UpalabdhaD/MGCplotter
Microbial Genome Circular plotting tool using Circos
UpalabdhaD/modulome-workflow
Workflow to download, process, and explore microbial RNA-seq data from NCBI SRA
UpalabdhaD/Promotech
Machine-learning-based general bacterial promoter prediction tool.
UpalabdhaD/R-for-bioinformatics
R course for bioinformatics
UpalabdhaD/SDG_LAB_DB
Data,Scripts and other NGS analysis materials for SDG LAB
UpalabdhaD/shape-based-TF-binding-prediction
A workflow to learn protein-DNA binding specificity from experimental peak data based on DNA shape.
UpalabdhaD/tidy-ncbi-genome-download
Collect and filter genomes downloaded using [ncbi-genome-downloa](https://github.com/kblin/ncbi-genome-download), change file names to safe names for down-stream processing (phylogenetic tree making etc.)
UpalabdhaD/tormes
Making whole bacterial genome sequencing data analysis easy
UpalabdhaD/training-collection
Collection of bioinformatics training materials