Pinned Repositories
16S_QIIME2
Snakemake based 16S QIIME2 pipeline
Abrigahit
Snakefile for assembly of metagenomes with Megahit and resistome profiling with Abricate
alignment
Spliced alignment evaluation software
ANF
Affinity Network Fusion
AutoCD
Automated synthetic microbial Community Design
Awesome-Bioinformatics
A curated list of awesome Bioinformatics libraries and software.
awesome-multi-omics
List of software packages for multi-omics analysis
burrito
A visualization tool for exploratory data analysis of metagenomic data
MIMOSA
Model-based Integration of Metabolite Observations and Species Abundances
picrust2
Code, unit tests, and tutorials for running PICRUSt2
marcelladane's Repositories
marcelladane/burrito
A visualization tool for exploratory data analysis of metagenomic data
marcelladane/picrust2
Code, unit tests, and tutorials for running PICRUSt2
marcelladane/16S_QIIME2
Snakemake based 16S QIIME2 pipeline
marcelladane/AutoCD
Automated synthetic microbial Community Design
marcelladane/bhattlab_workflows
Computational workflows for metagenomics tasks, by the Bhatt lab
marcelladane/bioinformatics_curriculum
Some ideas on things to learn to get started with bioinformatics
marcelladane/DAtest
Compare different differential abundance and expression methods
marcelladane/DeepCry
Neonatal Cry Detector
marcelladane/dowhy
DoWhy is a Python library for causal inference that supports explicit modeling and testing of causal assumptions. DoWhy is based on a unified language for causal inference, combining causal graphical models and potential outcomes frameworks.
marcelladane/dRNASb
marcelladane/dualrnaseq
Analysis of Dual RNA-seq data - an experimental method for interrogating host-pathogen interactions through simultaneous RNA-seq.
marcelladane/EconML
ALICE (Automated Learning and Intelligence for Causation and Economics) is a Microsoft Research project aimed at applying Artificial Intelligence concepts to economic decision making. One of its goals is to build a toolkit that combines state-of-the-art machine learning techniques with econometrics
marcelladane/gapseq
Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
marcelladane/kraken2_classification
Snakemake workflow for metagenomic classification with Kraken2
marcelladane/mare
Microbiota Analysis in R Easily
marcelladane/microbiome-toolbox
Early Life Microbiome Toolbox
marcelladane/MicrobiomeAnalystR
A companion R package for the MicrobiomeAnalyst web server
marcelladane/motif-domain_scripts
Preprocessing steps of the PHISTO database and the generation and enrichment of domain-domain and motif-domain combinations
marcelladane/PLSDAbatch
R package for batch effect correction
marcelladane/r4ds
R for data science: a book
marcelladane/SBW2022
This is a teaching material for scRNAseq workshop within SBW2022
marcelladane/seurat
R toolkit for single cell genomics
marcelladane/sleepwalk
Exploring dimension-reduced embeddings
marcelladane/snakemake-workflow-tool
How to package up a Snakemake workflow as a command-line tool
marcelladane/taxumap
marcelladane/TCGA_analysis
marcelladane/tourmaline
Amplicon sequence processing workflow using QIIME 2 and Snakemake
marcelladane/training-collection
Collection of bioinformatics training materials
marcelladane/workshop-reproducible-research
NBIS/ELIXIR course: Tools for Reproducible Research
marcelladane/workshop_omics_integration
Workshop in omics integration and systems biology