leipzig

awesome-reproducible-research

A curated list of reproducible research case studies, projects, tutorials, and media

berrylogo

a better seqLogo

clk

Refactor and test of robustness of Funnell "CLK-dependent exon recognition and conjoined gene formation revealed with a novel small molecule inhibitor"

m6a

Reproduction/refactor of Dominissini et al Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq

metadata-in-rcr

code and data related to "The Role of Metadata in Reproducible Computational Research"

opensnp

Can we validate published genome-wide association studies of common human phenotypes using the relatively small volunteered data publicly available in OpenSNP? Binderized!

placenta

Reproduction of Leiby et al. placental microbiome paper

SandwichesWithSnakemake

This is a beginner's tutorial to Snakemake

snakemake-example

RNA-Seq Snakemake example with Jekyll homepage creation

leipzig/SandwichesWithSnakemake

This is a beginner's tutorial to Snakemake

leipzig/dryad-repo

Dryad is a repository for data underlying scientific literature. Dryad allows investigators to validate published findings, explore new analysis methodologies and repurpose the data for research questions unanticipated by the original authors. The core code of Dryad comes from the DSpace repository software. Developers using the Dryad code should first familiarize themselves with DSpace. Documentation specific to the Dryad codebase can be found in the Dryad wiki.

leipzig/rchive

An comprehensive archive of genomic data structured and stored as R data objects

leipzig/Vennerable

Vennerable provides Venn diagrams in R. It displays Venn and Euler diagrams for up to 9 different sets and using a variety of geometries. It allows the display of area-weighted Venn diagrams and allows fine graphical control over the result.

leipzig/bakthat

Bakthat is a MIT licensed backup framework written in Python, it's both a command line tool and a Python module that helps you manage backups on Amazon S3/Glacier and OpenStack Swift. It automatically compress, encrypt (symmetric encryption) and upload your files.

leipzig/bank_wages_regression

leipzig/Bio-Microarray

Initial repository for microarray-based tools (may be renamed)

leipzig/career_mds

multidimensional scaling of career paths

leipzig/coffee_cluster

coffee market segmentation cluster analysis

leipzig/csv-parse-cutplace2

leipzig/DEGandMore

Analyses related to differential gene expression and functional annotation

leipzig/django-dbtemplates

Django template loader for database stored templates with extensible cache backend

leipzig/django-haystack

Modular search for Django. Currently v2.1.1-dev.

leipzig/inheritance

inheritance models for mendelian diseases

leipzig/kaggle_world_univ_rankings

leipzig/laundry_logit

multinomial logistic regression on laundry detergent loyalty

leipzig/moma_collection

The Museum of Modern Art (MoMA) collection data

leipzig/mvGSEA

Multiplevariate GSEA using logistic regression models

leipzig/phl-opa

A thin wrapper for the Philadelphia Office of Property Assessment API

leipzig/reproducibility-guide

leipzig/scds

Slowly-Changing Dimension Store (prototype)

leipzig/sem_debate

debate structural equation modeling

leipzig/SnpEff

leipzig/TCGA-discriminant-analysis

Linear Discriminate Analysis of TCGA breast cancer expression data

leipzig/text2dna

Automatically exported from code.google.com/p/text2dna

leipzig/UpSetR

An R implementation of the UpSet set visualization technique published by Lex, Gehlenborg, et al..

leipzig/VariantAnnotation

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/VariantAnnotation.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=VariantAnnotation.

leipzig/VariantFiltering

Bioconductor VariantFiltering package

leipzig/varify

Clinical DNA Sequencing Analysis and Data Warehouse

leipzig/varify-data-warehouse

Data model and loading pipeline for Varify