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bam-readcount

count DNA sequence reads in BAM files

bamreadcountr

wrapper and parser for bam readcount

basenji

Sequential regulatory activity predictions with deep convolutional neural networks.

climate_health

Personal project to evaluate the effects of climate change on population health

computational_intro

Originally compiled this document for my current lab to share with incoming students and staff

ecbm-e4060-covid-interactions

ellen_collab

ffq

A tool to find sequencing data and metadata from public databases.

hatchet-paper

Related to (Zaccaria and Raphael, 2018), the repository contains the simulated data, the results of all methods involved in the comparison, the results of HATCHet on the prostate and pancreas cancer datasets, and all data and analysis related to these last two cancer datasets.

intro-to-chipseq

Intro to ChIPseq using HPC

karini925.github.io

github pages for https://karini925.github.io/

ldpred-funct

Here we develop the software for the method LDpredfunct described in https://www.biorxiv.org/content/early/2018/07/24/375337

literature_review

Review of literature relevant to cancer genomics and survival analysis

lncrnas_tcga

Code I have used throughout my Masters analyzing TCGA clinical and RNA-Seq datasets to discover lncRNA prognostic markers

maftools

Summarize, Analyze and Visualize MAF files from TCGA or in house studies.

ml-course-notes

🎓 Sharing course notes on all topics related to machine learning, NLP, and AI.

mutecttitan2pyclone

R script to prepare inputs for PyClone

palimpsest

An R package for studying mutational and structural variant signatures along clonal evolution in cancer.

phylogicndt

spliceogen

survival_analysis_tutorial

test-github

making repo just to practice

tidy-tuesday

tracksig

A framework to infer mutational signatures in cancer over time

vgea

VGEA (Viral Genomes Easily Analyzed) is a pipeline for analysis of RNA virus next-generation sequencing data.

vorf

Efficient viral genome assembly using RNA-seq reads