mbernste

SpatialCorr

SpatialCorr: Identify gene sets with spatially varying correlation

SpatialCorr-sim

SpatialCorr-sim: Simulate spatial transcriptomics data with spatially varying correlation

mbernste.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

GSVApy

A Python wrapper around the GSVA algorithm

hypothesis-driven-SRA-queries

Find structured-datasets from within the Sequence Read Archive

onto_lib

Tools for loading and manipulating ontologies in Python

cello-dev

Refactoring of code used to develop CellO

gene-word-vector-exploration

normalize-umi

Python functions for various normalization procedures for UMI counts data

anna-karenina-beta-cell

autoPLIER-analysis

Analysis for the autoPLIER project

condor-tools

Tools for managing HTCondor jobs with Python

COVID-19-ARDS-analysis

dash-clustergrammer

A Clustergrammer component for Dash

DE-analysis

deconvolution-based-survival-prediction

dev-sca

Development of SCA

differentiating-islet-analysis

find-cell-line-samples-for-target-genes

GOSeqPy

A Python wrapper around GOSeq

intergenic-rna-seq-reads

MAGIC

MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.

nfat-multi-map-reads-analysis

phd-thesis

My Ph.D. thesis

pygraphviz

Python interface to Graphviz graph drawing package

scanpy

Single-Cell Analysis in Python. Scales to >1M cells.

semantic-components-analysis

shannonca

Information-based dimensionality reduction

SpatialCorr-dev

SRApy

Tools for downloading and processing RNA-seq data in the Sequence Read Archive