sjessa
Computational biologist & post-doc at Stanford: interested in the brain, functional genomics, and open science.
post-doc @kundajelab @GreenleafLabStanford Unviersity
Pinned Repositories
braindex
A web portal for exploring scRNAseq data in the developing brain, including our in-house atlas of the E10-P6 forebrain and brainstem
G34-gliomas
Cell-of-origin analysis for "Histone H3.3G34-mutant interneuron progenitors co-opt PDGFRA for gliomagenesis" (Chen*, Deshmukh*, Jessa*, Hadjadj*, et al, Cell, 2020)
HGG-oncohistones
Analysis for "K27M in canonical and noncanonical H3 variants occurs in distinct oligodendroglial cell lineages in brain midline gliomas" (Jessa et al, Nature Genetics, 2022)
chromswitch
An R/Bioconductor package for detecting chromatin state switches
cytokit
Toolkit for analyzing single cell RNA-seq data
cytoscope
A Shiny app for visualizing and exploring single cell RNA-sequencing data
fair-ML
An exploration of methods for fair machine learning
ggmin
Clean, minimalist theme for ggplot2 (+ a variant designed for Powerpoint)
resources
Resources and tools for reproducible research with R
rr
Custom, lightweight template workflow for reproducible research projects in R
sjessa's Repositories
sjessa/cytoscope
A Shiny app for visualizing and exploring single cell RNA-sequencing data
sjessa/chromswitch
An R/Bioconductor package for detecting chromatin state switches
sjessa/ggmin
Clean, minimalist theme for ggplot2 (+ a variant designed for Powerpoint)
sjessa/resources
Resources and tools for reproducible research with R
sjessa/rr
Custom, lightweight template workflow for reproducible research projects in R
sjessa/cytokit
Toolkit for analyzing single cell RNA-seq data
sjessa/fair-ML
An exploration of methods for fair machine learning
sjessa/rosalind
solutions to the bioinformatics learning platform: http://rosalind.info/
sjessa/chromswitch-analysis
Code and data to accompany the chromswitch paper, "chromswitch: A flexible method for detecting chromatin state switches" (Jessa and Kleinman, Bioinformatics, 2018)
sjessa/ACTINN
sjessa/expands
Expanding Ploidy and Allele Frequency on Nested Subpopulations (expands) characterizes coexisting subpopulations in a single tumor sample using copy number and allele frequencies derived from exome- or whole genome sequencing input data.
sjessa/ggnet
Network visualization with ggplot2
sjessa/morin-rotation
Rotation with Morin lab.
sjessa/NucleoATAC
nucleosome calling using ATAC-seq
sjessa/Pando
Multiome GRN inference.
sjessa/sjessa
GitHub profile README
sjessa/super
An R package implementing supervised scores for cluster analysis results