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2016-summer-workshop

ISCB DC Area Regional Student Group - Summer 2016 Workshop

altanalyze

AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.

atac_dnase_pipelines

ATAC-seq and DNase-seq processing pipeline

bcl2fastq-docker

bioinf545

ATAC-seq lab for BIOINF545

cellranger-docker

Docker container for Cell Ranger

cicero-release

diffngs

R scripts to identify differential regions in bigwig datasets of ChIP-seq, ATAC-seq, etc.

docker_test

Test for Making Docker File

ezmisc

ez Zhu's miscellaneous R functions

flair

Full-Length Alternative Isoform analysis of RNA

interactive_pca_explorer

Shiny app for exploring a PCA

ipynb-lamanno2016

Notebook and examples related to La Manno and Gyllborg et al. 2016

iterativewgcna

Extension of the WGCNA program to improve the eigengene similarity of modules and increase the overall number of genes in modules.

kallisto

Kallisto Docker

kallisto-nf

A nextflow implementation of Kallisto & Sleuth RNA-Seq Tools

monocle-release

nanoporeseq

R-Toolbox for Nanopore Pipeline: Automated Analysis of cDNA Sequencing Data

ngsane

Analysis Framework for Biological Data from High Throughput Experiments

oneliners

Useful bash one-liners for bioinformatics.

ont_tutorial_pinfish

This tutorial demonstrates how the Pinfish software can be used with Nanopore cDNA sequence data to discover gene isoforms

pergola

A tool for the visualization and analysis of longitudinal behavioral data

pici-scrnaseq

PICI single cell RNA-seq container

pyenv

Simple Python version management

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.

scatac

Multiplex single-cell ATAC-seq analysis pipeline (Ren Lab under development)

scde

R package for analyzing single-cell RNA-seq data

scrna-seq-tcc-prep

Preprocessing of single-cell RNA-Seq data for input to kallisto

scrna.seq.course

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

simlr

Single-cell Interpretation via Multi-kernel Learning (R code in master branch, Matlab code in matlab branch), implementations of the method published in http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.4207.html.