AmyOlex

Chrono

Parsing time normalizations from text.

R-Scripts

This repository contains bits and bobs of various R-scripts and functions that I've written organized loosely by topic.

hPRLrI_TCGA

Scripts to download TCGA BRCA RNASeq data and process them to extract Chr5, align to genome, and get gene expression to identify a PRLR isoform of interest. Project done for Jackie Gribble for her PhD Dissertation.

NBSentimentClassifier

A sentiment classification script for drug reviews using NLTK Naive Bayes Classifier.

Python-Scripts

This repository contains helpful TCGA parsing scripts that are outside of the tcgaRC R class, such as python scripts.

WCCTR_RNASeq_Pipeline

General scripts to implement the RNASeq pipeline for WCCTR projects.

2017-09-22-vcu

bash_scripts

A random assortment of various bash scripts I've written.

bibnet-google-scholar-scraper

Boyd_SynCompounds_PI3K

Code to accompany the Boyd et al manuscript on Discovering Synergistic Compounds with BYL-719 in PI3K Overactivated Basal-like PDXs.

BrCa_cell_atlas_fork

Data processing and analysis related code associated with the study "A single-cell and spatially resolved atlas of human breast cancers".

Clark_Bos_2020_TregsOpposeIFNgReprogOfMyeloidCells

Code and data used to produce select figures in Clark et al 2020 "Regulatory T cells support breast cancer progression by opposing IFN-γ -dependent functional reprogramming of myeloid cells." published in Cell Reports.

clinicalBERT

repository for Publicly Available Clinical BERT Embeddings

FineTuneBERT

gdc_processing

git-novice

Software Carpentry introduction to Git for novices.

guide-to-n3c-v1

Research with the National COVID Cohort Collaborative (N3C: https://ncats.nih.gov/n3c)

manuscript_template

Template of a manuscript in Rmd

medinify

Python text classification package with a focus on medical text.

multitasking_transformers

Multitask Learning with Pretrained Transformers

Project_Repo_Template

RNA-seq-Analysis-Scripts

Contains scripts and programs designed to process RNA-seq data from FASTQ files through DE analysis.

rna-seq-qc

Rna-seq pipeline, From FASTQ to differential expression analysis...

RNASeqBits

An R library with bits and bobs to help in RNAseq analysis pipelines.

Samidurai-Das_mTOR_miRNA_Cardioprotection

Code and data for "Network Analysis of LncRNA-miRNA-mRNA Interaction in Rapamycin-Induced Cardioprotection against Myocardial Injury in Diabetic Rabbits"

SC2ATmd

Application for consensus clustering using replicate data sets and Figure of Merit.

TCGAsurvival

Scripts to analyze TCGA data

timenorm

tokenizations_fork

Robust and Fast tokenizations alignment library for Rust and Python https://tamuhey.github.io/tokenizations/

w2n

Convert number words (eg. twenty one) to numeric digits (21)