Pinned Repositories
2017-09-22-vcu
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.
RNASeqBits
An R library with bits and bobs to help in RNAseq analysis pipelines.
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/RNASeqBits
An R library with bits and bobs to help in RNAseq analysis pipelines.
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/medinify
Python text classification package with a focus on medical text.
AmyOlex/multitasking_transformers
Multitask Learning with Pretrained Transformers
AmyOlex/Project_Repo_Template
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/SeuratHelper
Helper functions for the Seurat toolkit for single-cell genomics
AmyOlex/seuratTools
Fork of the original cobriniklab/seuratTools package to fix some Seurat object changes in structure that the developers are not prioritizing at the moment. This package is mainly being used to convert mouse gene IDs in a Seurat object to human for use with CellPhoneDB and LIANA Cell-Cell Communication packages.
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)