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LIONS is a bioinformatic analysis pipeline which brings together a few pieces of software and some home-brewed scripts to annotate a paired-end RNAseq library to detect TE-intiated transcripts
RepEnrich is a method to estimate repetitive element enrichment using high-throughput sequencing data.
Stuff related to the "Genetically Modified Crops and Food Security" PLoS ONE paper
SICER: A clustering approach for identification of enriched domains from histone modification ChIP-Seq data
Link collection for absolute beginners in bioinformatics
Calculate various reproducibility scores.
An ensemble approach to accurately detect somatic mutations using SomaticSeq
AC-PCA: simultaneously performs dimension reduction and adjustment for confounding variation
Going thru the http://learnpythonthehardway.org book.
Fast Principal Component Analysis of Large-Scale Genome-Wide Data
Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis
Minimalist alternatives to "best practices" paper
Convolutional neural network analysis for predicting DNA sequence activity.
Large-scale Analysis of Recurrent Variants in noncoding Annotations
Attractor finding algorithm
implementing deep dream on video
Training and testing of DeepBind models.
Training and testing of DeepSEA models.
A collection of papers and books that Storey Lab members should read and others may find useful
A lightweight, extendible, easy to use Python package for deep dreaming and image generation with Caffe and CNNs.
Deep learning for identifying cis-regulatory elements and other applications
Bioconductor package for gene expression anti-profiles
A career planning guide.
Publicly-visible Langmead Lab resources
Alignment, Similarity, & Database Matching for DNA Motifs
mod of pvclust R package for major efficiency/speed improvements on large datasets
The Leek group guide to genomics papers