cemalley
I'm a bioinformatician and statistician at NEI, part of the NIH. PhD student at George Mason University. Special Volunteer at NCATS NIH.
National Institutes of HealthBesthesda, MD
Pinned Repositories
Biowulf_swarm
Utility scripts for creating and running swarm job files on NIH Biowulf.
Chen_methods
Analysis pipelines for Chen et al. manuscript
ISSCR_2019
Methods relating to my ISSCR 2019 abstract and poster (single cell RNASeq and trajectory inference)
Jovanovic_methods
Preprocessing and analysis pipeline for Jovanovic et al. astrocytes manuscript.
Novelty-coding
Assorted perl scripts for assorted purposes!
OrthoParser
These programs parse OrthoFinder output, generate group FASTA files, and gather descriptive stats.
scRNA-posters
Posters presented at conferences and symposiums
scRNASeq-bulkRNASeq
single cell and bulk RNASeq analysis scripts
Tristan_methods
Single cell RNA-Seq analysis for Tristan et al. manuscript
WES
GATK pipeline for whole exome sequencing iPSC samples
cemalley's Repositories
cemalley/scRNASeq-bulkRNASeq
single cell and bulk RNASeq analysis scripts
cemalley/OrthoParser
These programs parse OrthoFinder output, generate group FASTA files, and gather descriptive stats.
cemalley/Biowulf_swarm
Utility scripts for creating and running swarm job files on NIH Biowulf.
cemalley/Chen_methods
Analysis pipelines for Chen et al. manuscript
cemalley/ISSCR_2019
Methods relating to my ISSCR 2019 abstract and poster (single cell RNASeq and trajectory inference)
cemalley/Jovanovic_methods
Preprocessing and analysis pipeline for Jovanovic et al. astrocytes manuscript.
cemalley/Novelty-coding
Assorted perl scripts for assorted purposes!
cemalley/Tristan_methods
Single cell RNA-Seq analysis for Tristan et al. manuscript
cemalley/WES
GATK pipeline for whole exome sequencing iPSC samples
cemalley/ADRN-EH-Project
Pipeline materials for the Atopic Dermatitis Research Network and the project specializing in ezcema herpeticum.
cemalley/Ryu_cerebral_organoids
Data analysis code for Ryu et al. manuscript in progress on cerebral embryoid bodies and organoids
cemalley/scRNA-posters
Posters presented at conferences and symposiums
cemalley/Slamecka_methods
Methods for Slamecka et al. manuscript in progress - trophectoderm differentiation with bulk and single cell RNASeq.
cemalley/ASHG16
Scientific poster presented at ASHG 2016 conference
cemalley/ASHG17
Code & data for my poster at the ASHG 2017 conference.
cemalley/data-viz
Sample R/ggplot2 visualization solutions and styling options using data from bioinformatics and sequencing tools.
cemalley/data.table
R data.table for genomics data
cemalley/Deng_methods
Analysis scripts from analyzing Tao Deng et al. nociceptor iPSC data
cemalley/misc_biowulf
assorted biowulf scripts for future reference
cemalley/plink1.9
Plink 1.9 commands for quick reference
cemalley/randomforests
Python3 tests with RF methods
cemalley/RFmethods
RF methods for classification and regression with CV and noise removal
cemalley/scanpy_usage
Scanpy use cases.
cemalley/Unexpected_R_art
Unexpected abstract art from real data in R.