siyoo's repositories
AffyPipeTBI
Genotype Caller From Axiom CEL files
de_novo_mutation_calling_pipeline
de novo mutation calling pipeline
agilent_cgp_check
Check the contents of Agilent SureSelect Cancer CGP
cnvkit_pipeline
#cnv_analysis #cnvkit #snakemake
fpdf2
Simple PDF generation for Python
getMappedRawReads
This is a pipeline written in snakemake. This pipeline checks the mapped read in the bam file as proper pair. And then, extracts mapped reads from the original raw read fastq file that has not been preprocessed(adapter trim, quality trim, etc...).
MINE
Methylation (Whole Genome Bisulfite Sequencing) analysis pipelINE
MultiQC
Aggregate results from bioinformatics analyses across many samples into a single report.
NSSP
Non-human Species Smallrna-seq Pipeline
pipeline_cookiecutter
a template for pipelining
PrimerProbe
"PrimerProbe: Microbiome Primer Identification Tool"
reportlabbookcode
Code examples for the book, ReportLab: PDF Processing with Python
rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
screenrc
Repository for my .screenrc files
snakemake-aws-parallelcluster-slurm
Snakemake profile for running on AWS ParallelCluster with the Slurm scheduler
wes-pipeline
Pipeline for Whole Exome Sequencing data
YoosModules
my python modules