genostack's repositories
slurm
Slurm Kubernetes learning materials
list_of_recommender_systems
A List of Recommender Systems and Resources
jupyter-notebook-samples
Sample Jupyter notebooks demonstrating the IRKernel
gwas-power
R Functions to calculate power of GWAS studies for a single associated SNP, under various parameters. Suitable for classical (i.e. single-SNP single-trait) GWAS studies using linear regression models, i.e for quantitative traits.
eggnog-mapper_COGextraction
Extraction of COG functional classes and save the data in csv format
gbmunge
Munge GenBank files into FASTA and tab-separated metadata
velvet
Short read de novo assembler using de Bruijn graphs, as published in: D.R. Zerbino and E. Birney. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 18: 821-829
ghostz-gpu
A GPU-accelerated sequence homology search tool using database subsequence clustering
read-big-file-with-python
The first part of a case study in reading a large (21GB) text file with python.
metabolomics2018
Scripts & Data for XCMS Workshop, Metabolomics 2018 in Seattle
Microbiome-Diversity-Inspector
Microbiome Diversity Inspector - A platform for visual analysis of microbiome data.
blast-validate
BLAST-based validation of metagenomic sequence assignments
2bRAD_GATK
Genome-wide reference-based genotyping with 2bRAD
CSBB-v3.0
CSBB - Computational Suite For Bioinformaticians and Biologists
BamQC
Mapped QC analysis program
elastic_data
Elasticsearch datasets ready for bulk loading
witsGWAS
A pipeline for Human GWAS analysis that accomodates both Affymetrix (raw .CEL files) and Illumina (Plink binaries) data
shinyGEO
Gene Expression Omnibus Analysis with Shiny :microscope:
SWEEP
Sliding Window Extraction of Explicit Polymorphisms
single-cell-spark-demo
Experiments on Single Cell data from 10x Genomics using Apache Spark.
hcl-picker
:art: Colorpicker for data
organdiet
Metagenomics pipeline for human diet analysis using organelles genomes
scalability-reproducibility-chapter
Data and workflow examples
2018-03-06-ibioic
Teaching materials for 6-7th March 2018 delivery of introductory bioinformatics training course for IBioIC.
speedseq
A flexible framework for rapid genome analysis and interpretation
DNA-Sequence-visualization
DNA sequence Visualization for detecting most affected protein for various types of cancer. This visualization is done using D3.js
Exploratory_Data_Analysis_Visualization_Python
Data analysis and visualization with PyData ecosystem: Pandas, Matplotlib Numpy, and Seaborn