Pinned Repositories
2017-09-22-vcu
bash_scripts
A random assortment of various bash scripts I've written.
Chrono
Parsing time normalizations from text.
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.
R-Scripts
This repository contains bits and bobs of various R-scripts and functions that I've written organized loosely by topic.
WCCTR_RNASeq_Pipeline
General scripts to implement the RNASeq pipeline for WCCTR projects.
AmyOlex's Repositories
AmyOlex/Chrono
Parsing time normalizations from text.
AmyOlex/R-Scripts
This repository contains bits and bobs of various R-scripts and functions that I've written organized loosely by topic.
AmyOlex/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.
AmyOlex/NBSentimentClassifier
A sentiment classification script for drug reviews using NLTK Naive Bayes Classifier.
AmyOlex/Python-Scripts
This repository contains helpful TCGA parsing scripts that are outside of the tcgaRC R class, such as python scripts.
AmyOlex/WCCTR_RNASeq_Pipeline
General scripts to implement the RNASeq pipeline for WCCTR projects.
AmyOlex/2017-09-22-vcu
AmyOlex/bash_scripts
A random assortment of various bash scripts I've written.
AmyOlex/bibnet-google-scholar-scraper
AmyOlex/Boyd_SynCompounds_PI3K
Code to accompany the Boyd et al manuscript on Discovering Synergistic Compounds with BYL-719 in PI3K Overactivated Basal-like PDXs.
AmyOlex/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".
AmyOlex/CCTR691_Fall2024
test
AmyOlex/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.
AmyOlex/clinicalBERT
repository for Publicly Available Clinical BERT Embeddings
AmyOlex/FineTuneBERT
AmyOlex/gdc_processing
AmyOlex/git-novice
Software Carpentry introduction to Git for novices.
AmyOlex/guide-to-n3c-v1
Research with the National COVID Cohort Collaborative (N3C: https://ncats.nih.gov/n3c)
AmyOlex/manuscript_template
Template of a manuscript in Rmd
AmyOlex/medinify
Python text classification package with a focus on medical text.
AmyOlex/multitasking_transformers
Multitask Learning with Pretrained Transformers
AmyOlex/Project_Repo_Template
AmyOlex/rna-seq-qc
Rna-seq pipeline, From FASTQ to differential expression analysis...
AmyOlex/RNASeqBits
An R library with bits and bobs to help in RNAseq analysis pipelines.
AmyOlex/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"
AmyOlex/SC2ATmd
Application for consensus clustering using replicate data sets and Figure of Merit.
AmyOlex/TCGAsurvival
Scripts to analyze TCGA data
AmyOlex/timenorm
AmyOlex/tokenizations_fork
Robust and Fast tokenizations alignment library for Rust and Python https://tamuhey.github.io/tokenizations/
AmyOlex/w2n
Convert number words (eg. twenty one) to numeric digits (21)