Pinned Repositories
3C_tutorial
Simple codes and lines to process 3C/Hi-C data
agent
Lift same species genome co-ordinates from one assembly to another
Axiom-LiftOver-BLAST
Coordinate conversion of Axiom SNP array markers using BLAST
bioinfo-tools
Just a collection of (often poor) scripts to do various bits of bioinformatics stuff I find myself needing to do.
bioinformatics-workflows
minimal example implementations for bioinformatics workflow managers
bionano_tools
Helper scripts for working with Bionano data
BioNanoAnalyst
BioNanoAnalyst is a tool providing GUI to assess the genome assembly quality using BioNano data.
BLUP
Best Linear Unbiased Prediction (BLUP) calculations on multi-year and multi-location phenotype data
Explore-phenotype
The script takes multi-year, multi-replication enviorment data as input and does exploratory analyisis (histogram, box plot), calculates baisc statistcs (mean, SD, missingness) and perform imputation (save imputed phenotype)
variant-calling-bwa-gatk4
Reads to variants workflow involving fastp-BWA-GATK
avdanurag's Repositories
avdanurag/BLUP
Best Linear Unbiased Prediction (BLUP) calculations on multi-year and multi-location phenotype data
avdanurag/Explore-phenotype
The script takes multi-year, multi-replication enviorment data as input and does exploratory analyisis (histogram, box plot), calculates baisc statistcs (mean, SD, missingness) and perform imputation (save imputed phenotype)
avdanurag/variant-calling-bwa-gatk4
Reads to variants workflow involving fastp-BWA-GATK
avdanurag/3C_tutorial
Simple codes and lines to process 3C/Hi-C data
avdanurag/agent
Lift same species genome co-ordinates from one assembly to another
avdanurag/Axiom-LiftOver-BLAST
Coordinate conversion of Axiom SNP array markers using BLAST
avdanurag/bioinfo-tools
Just a collection of (often poor) scripts to do various bits of bioinformatics stuff I find myself needing to do.
avdanurag/bioinformatics-workflows
minimal example implementations for bioinformatics workflow managers
avdanurag/bionano_tools
Helper scripts for working with Bionano data
avdanurag/BioNanoAnalyst
BioNanoAnalyst is a tool providing GUI to assess the genome assembly quality using BioNano data.
avdanurag/cue
Deep learning framework for SV calling and genotyping
avdanurag/diploidocus
Diploid genome assembly analysis tools
avdanurag/docker-builds
A collection of useful Docker builds
avdanurag/GenoToolBox
A box of genomics tools
avdanurag/hic-data-analysis-bootcamp
Workshop on measuring, analyzing, and visualizing the 3D genome with Hi-C data.
avdanurag/Maize_NC358
The repository for codes developed to generated the Maize NC358 assemblies and analyses.
avdanurag/nf-anvio-pangenome
Analyze a set of genomes with the anvi'o pangenome pipeline
avdanurag/Omni-C
Omni-C data processing documentation and scripts
avdanurag/OpenBioinformaticsWorkshops
Open courseware for workshops in applied bioinformatics
avdanurag/plant.annot
Annotation pipeline for plant genomes by PGSB
avdanurag/population_genomics
Scripts
avdanurag/protocols
Our laboratory repository
avdanurag/pyOverChain
a python pipeline to generate chain files between different genome assemblies for LiftOver.
avdanurag/teloclip
A tool for the recovery of unassembled telomeres from soft-clipped read alignments.
avdanurag/unix_oneliners
Scripts and one-liners to do data formatting and simple tasks required by fellow biologists.
avdanurag/vgp-assembly
VGP repository for the genome assembly working group