129e_rnaseq

Scripts of Garrido-Oter et. al, Modular traits of the Rhizobiales root microbiota and their evolutionary relationship with symbiotic rhizobia

assembly-annotation-pipeline

Plant genome assembly and annotation pipeline using snakemake

awesome-chatgpt-prompts

This repo includes ChatGPT prompt curation to use ChatGPT better. Newly added features includes Bioinformatics relevant tasks

bioinformatics-one-liners

Bioinformatics one liners from Ming Tang

c-codes_bioinformatics-algos

Bioinfomatics algorithms in C++

cmplot

📊 Circular and Rectangular Manhattan Plot

code_space_test

complexheatmap

Make Complex Heatmaps

cossa-workflows

CoSSA (Prodhomme et al., 2019) is a set of workflows used to identify quickly and efficiently haplotype specific SNPs linked to a trait of interest from Whole Genome Sequencing data. All the contributors to the design of these workflows are Danny Esselink, Charlotte Prodhomme and Theo Borm (Wageningen University UR Plant Breeding).

cossa_analysis_potato_testdata

Bash and python scripts for COSSA analysis of a test data for potato clones

dada2_pipeline

The pipeline for amplicon sequencing analysis based mainly on DADA2.

genome-wide-snp-discovery-using-rad-seq-data

A bash script based pipeline to analyze Rad-seq data to get SNPs.

hap10

A tool for reconstructing haplotypes polyploid genome using linked reads (10X Genomics).

haplotyping_linked_reads_tetraploids_potatotools

haplotyping_testing

jupyter

The repository contains script and notebook related to Statistics, Machine learning, Neural network, Deep learning, NLP, Numerical methods, and Automation.

learning_awk

Finally learning AWK instead of being annoyed at its syntax

machine_learning_bioinformatics_practice

nadiabaig

Config files for my GitHub profile.

nadiabaig-haplotyping-in-tetraploids_python_pipeline

Not fully functional at the moment. Code needs major changes

nextflow_pipelines_ngs

The set of NGS processing pipelines used at Babraham

pandas-cookbook

Recipes for using Python's pandas library

potato_c88

Chromosome-scale and haplotype-resolved assmebly of tetraploid cultiavetd potato with polyploidy graph binning

pytorch-deep-learning

Deep Learning (with PyTorch)

rhizobiales

Scripts of Garrido-Oter et. al, Modular traits of the Rhizobiales root microbiota and their evolutionary relationship with symbiotic rhizobia

short_scripts_ngs_data_processing

This repository consists of short python/bash scripts that you need at some point of your NGS data processing and analysis.

skill-assessments

Training requirements for joining projects

snp-cnv_detection_wgs

Bash pipeline for Single Nucleotide Polymorphism (SNP) and CNV detection in WGS data

snp_ngs_data_plotting

Python and R based scripts to plot your VCF, SNP and NGS data

solanum_hugassi_nuc_search

Short scripts for fetching nucleotide (FASTA), SRA (fastq), protein/gene information and Publication records from NCBI database for Solanum_Hugassii. Scripts can be modified to extract information for other species too.