Pinned Repositories
CellO
CellO: Gene expression-based hierarchical cell type classification using the Cell Ontology
MetaSRA-pipeline
MetaSRA: normalized sample-specific metadata for the Sequence Read Archive
monkeybread
Analyzing cellular niches in spatial transcriptomics data
GSVApy
A Python wrapper around the GSVA algorithm
hypothesis-driven-SRA-queries
Find structured-datasets from within the Sequence Read Archive
machine-learning
A Java library of machine learning algorithms.
mbernste.github.io
Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes
onto_lib
Tools for loading and manipulating ontologies in Python
SpatialCorr
SpatialCorr: Identify gene sets with spatially varying correlation
SpatialCorr-sim
SpatialCorr-sim: Simulate spatial transcriptomics data with spatially varying correlation
mbernste's Repositories
mbernste/SpatialCorr
SpatialCorr: Identify gene sets with spatially varying correlation
mbernste/mbernste.github.io
Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes
mbernste/SpatialCorr-sim
SpatialCorr-sim: Simulate spatial transcriptomics data with spatially varying correlation
mbernste/GSVApy
A Python wrapper around the GSVA algorithm
mbernste/hypothesis-driven-SRA-queries
Find structured-datasets from within the Sequence Read Archive
mbernste/onto_lib
Tools for loading and manipulating ontologies in Python
mbernste/cello-dev
Refactoring of code used to develop CellO
mbernste/gene-word-vector-exploration
mbernste/normalize-umi
Python functions for various normalization procedures for UMI counts data
mbernste/anna-karenina-beta-cell
mbernste/autoPLIER-analysis
Analysis for the autoPLIER project
mbernste/condor-tools
Tools for managing HTCondor jobs with Python
mbernste/COVID-19-ARDS-analysis
mbernste/dash-clustergrammer
A Clustergrammer component for Dash
mbernste/DE-analysis
mbernste/deconvolution-based-survival-prediction
mbernste/dev-sca
Development of SCA
mbernste/differentiating-islet-analysis
mbernste/find-cell-line-samples-for-target-genes
mbernste/GOSeqPy
A Python wrapper around GOSeq
mbernste/intergenic-rna-seq-reads
mbernste/MAGIC
MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.
mbernste/nfat-multi-map-reads-analysis
mbernste/phd-thesis
My Ph.D. thesis
mbernste/pygraphviz
Python interface to Graphviz graph drawing package
mbernste/scanpy
Single-Cell Analysis in Python. Scales to >1M cells.
mbernste/semantic-components-analysis
mbernste/shannonca
Information-based dimensionality reduction
mbernste/SpatialCorr-dev
mbernste/SRApy
Tools for downloading and processing RNA-seq data in the Sequence Read Archive