Deena-B

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

fluHA

For pipeline development starting with flu HA fasta files

gatk

Official code repository for GATK versions 4 and up

mitolin

Use mitochondrial sequence from single cells to determine cell lineage relationships

overview

General description of the group's goals, aims, projects, organizers, contributors, communication channels, key concepts, FAQs, etc

bioutils

provides common tools and lookup tables used primarily by the hgvs and uta packages

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

course-v3

The 3rd edition of course.fast.ai - coming in 2019

coursera_bioinf_spec_UCSD

Problems and Projects from Coursera's Bioinformatics Specialization from Pavel Pevzner and Phillip Compeau

cromwell

Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments

eutils

simplified searching, fetching, and parsing records from NCBI using their E-utilities interface

fastai

The fastai deep learning library, plus lessons and and tutorials

fastai_docs

dev notebooks (for docs see http://docs.fast.ai and https://github.com/fastai/fastai)

flu

A presentation with my main PhD and postdoc findings

hgvs

Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`

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

LearnPython_in1day

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

MonoVar

Single nucleotide variant (SNV) detection and genotyping algorithm for single-cell DNA sequencing data

pcam

The PatchCamelyon (PCam) deep learning classification benchmark.

python-docx

Create and modify Word documents with Python

pytorch

Tensors and Dynamic neural networks in Python with strong GPU acceleration

SiFit

Reconstructing phylogenetic tree from noisy mutation profile of single cells

uta

Universal Transcript Archive: comprehensive genome-transcript alignments; multiple transcript sources, versions, and alignment methods; available as a docker image

varactor

Visualization and analysis of single-cell RNA-seq data by alternative clustering