Name: Avantika Lal
Type: User
Company: @Genentech
Bio: Principal AI Scientist at Genentech. Formerly Insitro, NVIDIA, Stanford. I work on applications of deep learning and machine learning to genomics.
Twitter: lal_avantika
Location: California, USA
Blog: http://avantikalal.github.io/
Avantika Lal's Projects
DL based processing of atac-seq data
Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
Hackathon team: gene expression analysis for Covid-19
Examples of single-cell genomic analysis accelerated with RAPIDS
Single-Cell Analysis in Python. Scales to >1M cells.
SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.
Extracting mutational signatures via LASSO. The manuscript of the method is available as a preprint at: https://www.biorxiv.org/content/10.1101/384834v3
Training requirements for joining projects
Deep Learning based variant calling toolkit - https://clara-parabricks.github.io/VariantWorks/
A list of women tech speakers & organizers. Add yourself or others by submitting a PR! PS if you do add someone, make sure to tell them! :) #fempire