Shweta Pipaliya's repositories
bulk-rnaseq
This repo contains scripts and workflows for performing bulk transcriptomics analyses
ds-ml-day1
Python for Data Science and Machine Learning: day 1
GWAS-scripts
Bash scripts provided here to run various GWAS QC, Imputation, PCA, and association testing steps using PLINK, SMARTPCA, RStats and Visualization
amoebae
Script toolkit for identifying and classifying homologous gene/protein sequences
basic_bioinfor_scripts
Basic Scripts for Day to Day Bioinformatics
bonsai
Bonsai: Fast, flexible taxonomic analysis and classification
bowtie2
A fast and sensitive gapped read aligner
chatGPT
This folder contains Q&A sessions and recommendations from ChatGPT for various bioinformatics, genomics, machine-learning, coding-related tasks, and general biology inquiries. Kept as general-purpose notebook.
de-novo-genome-assembly
Scripts for genome assembly associated tasks - scripts and parameters set up for run on Compute Canada HPC
GWAS-pipeline
This is a general (somewhat comprehensive) description of the LNG GWAS pipeline which can be used to guide researchers on how-to run a GWAS.
helpful_commands
Command-line tools, commands, and code snippets for performing routine data processing and bioinformatics tasks
kingfisher-download
Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.
kraken2
The second version of the Kraken taxonomic sequence classification system
KrakenTools
KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files
Liftoff
An accurate GFF3/GTF lift over pipeline
MachineLearning_notes
Machine learning and deep learning resources
ncbi-genome-download
Scripts to download genomes from the NCBI FTP servers
python_DSML
course material from EPFL L&D's Python for Data Sciences and Machine Learning Course (Sep 21-23)
quast
Genome assembly evaluation tool
samtools
Tools (written in C using htslib) for manipulating next-generation sequencing data
scanpy
Single-cell analysis in Python. Scales to >1M cells.
training-collection
Collection of bioinformatics training materials
typhaon
A workflow for phylogenetic analysis of protein families.