All Published Workflows
28 workflows that have been reviewed and published
ATLAS - Three commands to start analyzing your metagenome data
Metagenome-atlas is a easy-to-use metagenomic pipeline based on snakemake. It handles all steps from QC, Assembly, Binning, t...
raw sequence reads
Genome assembly
Annotation track
checkm2
gunc
prodigal
snakemake-wrapper-utils
MEGAHIT
Atlas
BBMap
Biopython
BioRuby
Bwa-mem2
cd-hit
CheckM
DAS
Diamond
eggNOG-mapper v2
MetaBAT 2
Minimap2
MMseqs
MultiQC
Pandas
Picard
pyfastx
SAMtools
SemiBin
Snakemake
SPAdes
SqueezeMeta
TADpole
VAMB
CONCOCT
ete3
gtdbtk
h5py
networkx
numpy
plotly
psutil
utils
metagenomics
RINDTI: Simplifying Drug-Target Interaction Prediction with Protein Residue Interaction Networks
This repository aims to simplify the drug-target interaction prediction process which is based on protein residue interaction...
Amplicon data processing workflows for diversity analysis
This software makes use of the workflow management system Snakemake to build and integrate different amplicon workflows a...
Code for replicating "Right and left, partisanship predicts vulnerability to misinformation" by Dimitar Nikolov, Alessandro Flammini and Filippo Menczer
Introduction
Datasets
Link Sharing on Twitter
Political Valence
Misinformation
d...
Analysis pipeline associated with master's thesis on the population structure, demographic history and distribution of fitness effects of birches in Scandinavia.
Code and supplementary associated with master's thesis on the population structure, demographic history and the distribution ...
A snakemake for GTDB-tk
It uses GTDB-tk to taxonomically annotate your genomes and to build a tree. Run as follows:
dbdir="databases"
genome_dir="gen...
Benchmarking Machine Learning Methods for Identifying Mislabeled Data
This repo contains code for the maniscript Benchmarking machine learning methods for the identification of mislabeled data ...
A computational method to generate causal explanations for proteomic profiles using prior mechanistic knowledge in the literature, as recorded in cellular pathway maps.
This is a tool for pathway analysis of proteomic and phosphoproteomic datasets. CausalPath aims to identify mechanistic pathw...
Short Tandem Repeat (STR) Catalog Analysis Workflow
Active STRs Analysis This repository contains a Snakemake workflow for analyzing the regulatory and functional role of short ...
Amplicon data processing workflows for diversity analysis
This software makes use of the workflow management system Snakemake to build and integrate different amplicon workflows a...