Pinned Repositories
covid19_MD
My dashboard for zip code level analysis of COVID19 cases in Maryland
diffexpr
Porting DESeq2 into python via rpy2
diploid-contam
dotfiles-rs
This is a simple dot files manager for syncing dot files across machines.
fastq-tools
ridgeplot-py
plotting ridge plots with matplotlib
sequencing_tools
A python package storing different tools for different NGS operations
tgirt-dna-seq
wckdouglas's Repositories
wckdouglas/sequencing_tools
A python package storing different tools for different NGS operations
wckdouglas/fastq-tools
wckdouglas/tgirt_map
pipeline for RNA-seq using TGIRT total RNA-seq
wckdouglas/cfNA
wckdouglas/lab_notes
Repository for lab stuff
wckdouglas/ngs_qc_plot
Scripts for QC in NGS analyses
wckdouglas/bamsurgeon
tools for adding mutations to existing .bam files, used for testing mutation callers
wckdouglas/COSMOS2
Python Scientific Pipeline Management System
wckdouglas/deep_cfNA
Using deep learning to classify fragments from TGIRT-seq libraries of cell-free nucleic acids
wckdouglas/DNAbarcoding
A program to generate sets of sample/cell barcodes
wckdouglas/edgePy
A Python implementation of edgeR for differential expression analysis
wckdouglas/empirical-bayes-book
Introduction to Empirical Bayes: Examples from Baseball Statistics
wckdouglas/fastqe
FASTQ sequence quality visualisation with Emoji
wckdouglas/glmpca-py
generalized principal component analysis (GLM-PCA) implemented in python
wckdouglas/intervaltree
A mutable, self-balancing interval tree. Queries may be by point, by range overlap, or by range containment.
wckdouglas/Mining-the-Social-Web-3rd-Edition
The official online compendium for Mining the Social Web, 3rd Edition (O'Reilly, 2018)
wckdouglas/perbase
Per-base per-nucleotide depth analysis
wckdouglas/primer3-py
Simple oligo analysis and primer design
wckdouglas/py-debruijn
Python implementation of de Bruijn graph for genome assembly
wckdouglas/pyNormFinder
python reimplementation for NormFinder
wckdouglas/pytest-pysam
Example using pytest with pysam
wckdouglas/qci-api
Interface for QCI's API using Python's requests library
wckdouglas/qiaseq-smcounter-v2
wckdouglas/quicksect
a cythonized, extended version of the interval search tree in bx
wckdouglas/SalmonTE
SalmonTE is an ultra-Fast and Scalable Quantification Pipeline of Transpose Element (TE) Abundances
wckdouglas/snakemake-workflow-template
A cookiecutter template for a snakemake-workflow readme file
wckdouglas/tgirt_smRNA
Scripts for analyzing and modeling TGIRT-seq data on miRXplore miRNA reference
wckdouglas/tgirt_smRNA_correction
wckdouglas/umi_design
wckdouglas/whatshap
Read-based phasing of genomic variants, also called haplotype assembly