cyang-2014 Goto Github PK

psap-pipeline

publications

Scripts used in published papers

quantstrat-tutorial

beamer/knitr slides for quantstrat tutorial

r_meetup_aug25_2015_slidify

raceid

rawdata

repdata_peerassessment1

Peer Assessment 1 for Reproducible Research

ribodiff

RiboDiff: Tool to detect changes in translational efficiency based on ribosome footprinting data

riboseq

riboviz

Analysis and Visualization of Ribosome Profiling Data

rigraph

igraph R package

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.

rnaseq_using_shiny_markdown

Demo showing how shiny and markdown can be used to create an interactive report for RNAseq analysis using the edgeR and GOseq packages

rtsne

R wrapper for Van der Maaten's Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding

rufigs

sambamba

Tools for working with SAM/BAM data

scanpy

Single-Cell Analysis in Python. Scales to very high cell numbers.

scdd

R package to identify genes with differential distributions in single-cell RNA-seq

scde

R package for analyzing single-cell RNA-seq data

scenic

scikit-bio

scikit-bio is an open-source, BSD-licensed, Python package providing data structures, algorithms, and educational resources for bioinformatics.

scikit-learn

scikit-learn: machine learning in Python

scite

sclvm

scLVM is a modelling framework for single-cell RNA-seq data that can be used to dissect the observed heterogeneity into different sources, thereby allowing for the correction of confounding sources of variation.

scns-toolkit

Single cell network synthesis toolkit

screenprocessing

script

scripts used for preparing track files

scrna.seq.course

Analysis of single cell RNA-seq data course, Cambridge University, UK

scrnaseq-malaria

Codes associated with the Poran et al. paper titled "Single-cell RNA-seq reveals a signature of sexual commitment in malaria parasites".

sctda

An object oriented python library for topological data analysis of high-throughput single-cell RNA-seq data