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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)

bioutils

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

breastcancerproteomes-kaggle

Project plan

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

course-v3db

a place to keep my notebooks and project folders related to fastai DL part 1 v3 course

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

datasciencecoursera

Projects undertaken during Data Science Specialization (10 month) course on Coursera

datasharing

The Leek group guide to data sharing

dpmitolin

Use mitochondrial sequence from single cells to determine cell lineage relationships with deep learning

eutils

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

exp_fast

Experimenting with Git/Github, merge, rebase, etc

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

fluha

For pipeline development starting with flu HA fasta files

gatk

Official code repository for GATK versions 4 and up

hello-world

my first repository

hgvs

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

holbertonschool-python-camp

I'm now a Holberton Python Camp student

ili

Influenza like illness as an indicator of influenza virus attack rates

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

learn-bioinformatics

List of resources for learning bioinformatics, from beginner to advanced

learnpython_in1day

learnworkflow_newrepo1

menagerie-mysql-pd-demo

Python demo program and Jupyter notebook used to show Pandas, MySQL interactions, etc.