Deena Blumenkrantz's repositories
ATAC_mito_sc
single cell ATACseq pipeline
benchmarking_variant_callers
In this study, we perform systematic comparative analysis of seven widely-used SNV-calling methods, including SAMtools, the GATK Best Practices pipeline, CTAT, FreeBayes, MuTect2, Strelka2 and VarScan2, on both simulated and real single-cell RNA-seq datasets. We evaluate the performances of these tools in different read depths, genomic contexts, functional regions and variant allele frequencies.
biocommons.seqrepo
non-redundant, compressed, journalled, file-based storage for biological sequences
biopython
Official git repository for Biopython (converted from CVS)
dpmitolin
Use mitochondrial sequence from single cells to determine cell lineage relationships with deep learning
mitolin
Use mitochondrial sequence from single cells to determine cell lineage relationships
coursera_bioinf_spec_UCSD
Problems and Projects from Coursera's Bioinformatics Specialization from Pavel Pevzner and Phillip Compeau
fastai_docs
dev notebooks (for docs see http://docs.fast.ai and https://github.com/fastai/fastai)
Intro-to-rnaseq-hpc-O2
This repository has teaching materials for a 2 and 3-day Introduction to RNA-sequencing data analysis workshop using the O2 Cluster
menagerie-mysql-pd-demo
Python demo program and Jupyter notebook used to show Pandas, MySQL interactions, etc.
mito-genotyping
Repo for scripts for Ludwig et al mtDNA genotyping
python-docx
Create and modify Word documents with Python