Variant calling of WGS datasets
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Updated
Apr 18, 2022 - Shell
Variant calling of WGS datasets
Workflow for running PennCNV with Affymetrix platform files
Performed a differential gene expression analysis with RNA-seq that compares the expression in human control breast cancer cell lines with lines treated by silencing the NRDE2 gene. A Salmon + tximport + DESeq2 workflow was conducted to pursue this.
Set of scripts to process RAD-Seq HTS data on computing grids like MetaCentrum.
This repository will house the scripts used to analyze and represent genomic and temperature data for my dissertation.
slurm and pbs scripts for genome, metagenome, transcriptome analysis.
Computational analysis of the evolutionarily conserved Missing In Metastasis / Metastasis Suppressor 1 gene predicts novel interactions, regulatory regions and transcriptional control (Petrov et al. 2019 Sci Rep)
Convert from fasta to phylip format and generate partitioned data if needed
Workflow for running PennCNV with Illumina platform final report
Metagenomic functional annotation pipeline
Metabarcoding analysis pipeline, using DADA2 and qiime2
A pipeline for metagenomic analysis
A Python workflow for taking chemicals, finding the genes they interact with, and mapping the communities of genetic interactions.
Bu sayfada Biyoinformatik analizler ile ilgili eğitim materyalleri bulunmaktadır.
This pipeline processes high-throughput sequencing data (PE/SE) through QC,trim/filter,alignment,counting etc via sequential stages, with individual samples run in parallel via submission to a Slurm queue.
Scripts used to generate the analyses and figures in the paper "Systems-based approach for optimization of a scalable bacterial ST mapping assembly-free algorithm".
A generic best practice workflow for processing human Oxford Nanopore Technologies (ONT) sequencing data.
Intra-Clade Dynamics of Candidatus Accumulibacter phosphatis over Time using de novo Extraction of Strains from Metagenomes
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