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psinanopore

python

My Python Examples

python-cookbook

Code samples from the "Python Cookbook, 3rd Edition", published by O'Reilly & Associates, May, 2013.

python-implement-fast-blast-basic-local-alignment-search-tool

Python implementation of Basic Local Alignment Search Tool (BLAST) , which is the core algorithm in sequence alignmenrt for genomes.

python-machine-learning-book-2nd-edition

The "Python Machine Learning (2nd edition)" book code repository and info resource

python-programming-exercises

100+ Python challenging programming exercises

python3-cookbook

《Python Cookbook》 3rd Edition Translation

pythonrobotics

Python sample codes for robotics algorithms.

r2vr

R to Virtual Reality

racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. http://genome.cshlp.org/content/early/2017/01/18/gr.214270.116

rainbow-is-all-you-need

Rainbow is all you need! Step-by-step tutorials from DQN to Rainbow

rats

Relative Abundance of Transcripts: An R package for the detection of Differential Transcript isoform Usage.

rattle

Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing

recurrentmutationstats

This contains code for statistical analysis of recurrent mutations in whole genome sequencing data.

regtools

Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.

replacing-bash-scripting-with-python

Guide on using using python for administrative scripting

rna-seq-analysis

RNAseq analysis notes from Tommy Tang

rna-seq-benchmarking

R codes for the benchmarking of 2 aligners (STAR and Kallisto) and 6 differential expression analysis methods (DESeq2, edgeR, limma-voom, CD, t-test, fold change) in RNA-Seq

rna-seq-diff-exprn

RNA-Sequencing data differential expression analysis pipeline. Performs: genome coverage (via bedtools and HTSeq), generates Circos code and plots, differential expression (via DESeq and NOISeq), structural variant detection (e.g. fusion genes, via SVDetect) and differential exon usage (via DEXSeq).

rna-seq-example

An analysis of Arabidopsis RNA-seq data (hy5 mutant and wt, two replicates each; SRA accession SRX029582)

rna-seq-scripts

This is a collection of small scripts built by the Lenz lab to make RNA sequencing tasks more efficient.

rnaseq-workflow

A repository for setting up a RNAseq workflow

rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

rosalind-1

Solutions to Rosalind Bioinformatics Problems

rseqc

RNA-Seq Quality Control: Generates QC metrics for RNA-Seq data using the RSeQC suite; a graphical report of these metrics can be viewed on the DNAnexus website

rtsne

An R package for t-SNE (t-Distributed Stochastic Neighbor Embedding)

scallop

Scallop is a reference-based transcriptome assembler for RNA-seq

scalloptest

sccaller

Single Cell Caller (SCcaller) - Identify single nucleotide variations (SNVs) from single cell sequencing data

scmnase