All Published Workflows
4 workflows that have been reviewed and published
Cell cycle analysis of single-cell proteomic and transcriptomic data for the FUCCI cell model
This repository contains the code used to perform the single-cell proteogenomic analysis of the human cell cycle . This s...
Snakemake workflow for the mapping and quantification of miRNAs and isomiRs from miRNA-Seq libraries.
MIRFLOWZ is a [Snakemake][snakemake] workflow for mapping miRNAs and isomiRs.
Installation
Cloning the repos...
Snakemake workflow: Meta-analysis of GWAS of gestational duration, preterm and post-term deliveries (EGG Consortium)
This repository contains code for Genetic effects on the timing of parturition and links to fetal birth weight .
Pol ...
Sample annotation
Analysis
Gene report
plink2
BCFtools
BEDTools
ggtree
GWAS
Pandas
pLink
Quant
Snakemake
Variant Effect Predictor (VEP)
coloc
cowplot
data.table
dendextend
dplyr
ggplot2
ggrepel
ggtern
gridExtra
kableExtra
knitr
metafor
plyr
scales
showtext
tidyr
tidyverse
numpy
scipy
Genetic variation
preeclampsia
Shotgun metagenomic sequencing processing pipeline
Snakemake
Apptainer/Singularity : while in many cases we do provide conda envs the only method of execution we...
Gene ID
Gene prediction
Gene report
ABRicate
AMRFinderPlus
antismash-lite
bracken
hmmer
antiSMASH
BBMap
Bowtie 2
cloudSPAdes
CoverM
dbCAN2
FastQC
humann
kraken2
Krona
MetaErg
MetaPhlAn
MetaQUAST
metaspades
MetaWRAP
plasmidspades
QUAST
rnaspades
SAMtools
seqkit
Snakemake
SortMeRNA
SPAdes
RGI
Metagenomic sequencing