Al3n70rn's repositories
adv-r
Advanced R programming: a book
affyLumCNA
Copy Number Alterations: Preprocessing, integration, and analysis of Affymetrix and Illumina data
ballgown
isoform-level differential expression analysis in R
chip-seq_preprocess
A preprocessing pipeline for ChIP-seq, including alignment, quality control, and visualization.
CNVworkshopEBI
hands-on for NGS/SNParray CNV call trainning
copynumbR
An R package for copy number data (aCGH, SNP arrays)
derfinder
R package for DER Finder, a method for differential expression analysis of RNA-seq data
EgoNet
Subnetwork selection from large-scale biological network based on gene expression data
focalCall
R-package for the detection and annotation of focal CNAs
GRIDITH
Deciphering clonality in aneuploid tumors
ImageAnalyzer
MATLAB texture analysis tool for medical images
lifelines
Survival analysis in Python
msisensor
microsatellite instability detection using paired tumor-normal
pipelines_for_ChIP-seq_analysis
Pipelines for ChIP-seq analysis, such as peak calling, differential enrichment detection, and pausing index calculation for PolII.
pytenn2014_tutorial
PyTennessee 2014: Statistical Data Analysis in Python
qqman
R code for creating Manhattan plots and Q-Q plots for GWAS
RESprog
Program directory RESPONSIFY
rnaseq_tutorial
An educational tutorial and working demonstration pipeline for RNA-seq analysis including an introduction to: cloud computing, next generation sequence file formats, reference genomes, gene annotation, expression analysis, differential expression analysis, alternative splicing analysis, data visualization, and interpretation.
SNPchip
This package defines methods for visualizing high-throughput SNP array data for copy number applications
statistical-analysis-python-tutorial
Statistical Data Analysis in Python
SubcloneSeeker
Computational Framework to reconstructing tumor clone structures
SwitchSeq
A tool to identify, annotate and visualise splicing switch events from RNA-seq data
TeachingMaterial
RNA-seq data analysis practical
TeachingMaterial-1
Various teaching material
tophat_cufflinks_rnaseq
RNA-Seq Analysis Pipeline: Maps RNA-Seq data and assesses expression using Tophat and Cufflinks