Al3n70rn's repositories
2014
Official content for the Fall 2014 Harvard CS109 Data Science course
ascat
ASCAT copy number R package
awesome-R
A curated list of awesome R frameworks, packages and software.
Clonal_Analysis
Analysis Pipeline for Dissecting the Clonal Origins of Childhood Acute Lymphoblastic Leukemia By Single-Cell Genomics
ComplexHeatmap
make complex heatmaps as well as self define annotation graphics
d3Network
Tools for creating D3 JavaScript network graphs from R.
deepTools
Tools to process and analyze deep sequencing data.
epitopefinder
Python package for mapping epitopes to sequences
erythroid_ir_analysis
Intron retention analysis for erythroid development (RNA-Seq)
example
example
ggBrain
Helper functions for making brain image figures with ggplot
ggExtra
Adding marginal histograms to ggplot2, and more ggplot2 enhancements
growcut
Python implementation of the growcut algorithm.
HER2-heterogeneity
Supplementary information for Ng et al, Intra-tumor genetic heterogeneity and alternative driver genetic alterations in breast cancers with heterogeneous HER2 gene amplification
jbryer.github.com
Jason Bryer's Github projects
kma
Keep Me Around: Intron Retention Detection
labs
Scripts for PH525x: Data Analysis for Genomics
LearnBioconductor
Training material for a Fall, 2014 introductory R / Bioconductor course
MACS
MACS -- Model-based Analysis of ChIP-Seq
mapmuts
Map mutations and infer amino-acid preferences from overlapping paired-end amino acid reads
metaseq
Framework for integrated analysis and plotting of ChIP/RIP/RNA/*-seq data
netuser15
igraph tutorial at the userR 2015 conference
NetworkAnalysisTalk_April2015
talk and code for 17 April 2015 'Meet the Geek' seminar series
RMI
R in medical imaging
Rmodules
A R statistical analysis module plugin for tranSMART
sciclone
An R package for inferring the subclonal architecture of tumors
scRNA-Seq_papers
A list of single-cell RNA-Seq papers from our reading group