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Name: Deena Blumenkrantz
Type: User
Bio: I'm interested in how genetic mutations affect phenotypes. My background is in influenza virology. Twitter: @Deena_B7
Location: San Francisco, CA, USA
Name: Deena Blumenkrantz
Type: User
Bio: I'm interested in how genetic mutations affect phenotypes. My background is in influenza virology. Twitter: @Deena_B7
Location: San Francisco, CA, USA
single cell ATACseq pipeline
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.
non-redundant, compressed, journalled, file-based storage for biological sequences
Official git repository for Biopython (converted from CVS)
provides common tools and lookup tables used primarily by the hgvs and uta packages
Project plan
Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
The 3rd edition of course.fast.ai - coming in 2019
a place to keep my notebooks and project folders related to fastai DL part 1 v3 course
Problems and Projects from Coursera's Bioinformatics Specialization from Pavel Pevzner and Phillip Compeau
Scientific workflow engine designed for simplicity & scalability. Trivially transition between one off use cases to massive scale production environments
Projects undertaken during Data Science Specialization (10 month) course on Coursera
The Leek group guide to data sharing
Use mitochondrial sequence from single cells to determine cell lineage relationships with deep learning
simplified searching, fetching, and parsing records from NCBI using their E-utilities interface
Experimenting with Git/Github, merge, rebase, etc
The fastai deep learning library, plus lessons and and tutorials
dev notebooks (for docs see http://docs.fast.ai and https://github.com/fastai/fastai)
A presentation with my main PhD and postdoc findings
For pipeline development starting with flu HA fasta files
Official code repository for GATK versions 4 and up
my first repository
Python library to parse, format, validate, normalize, and map sequence variants. `pip install hgvs`
I'm now a Holberton Python Camp student
Influenza like illness as an indicator of influenza virus attack rates
This repository has teaching materials for a 2 and 3-day Introduction to RNA-sequencing data analysis workshop using the O2 Cluster
List of resources for learning bioinformatics, from beginner to advanced
Python demo program and Jupyter notebook used to show Pandas, MySQL interactions, etc.
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.