All Published Workflows

53 workflows that have been reviewed and published

dna-seq-varlociraptor
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A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse, germline, pedigree, populations) via the unified statistical model of Varlociraptor.
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public

A Snakemake workflow for calling small and structural variants under any kind of scenario (tumor/normal, tumor/normal/relapse...
JSON raw sequence reads Variant calling genetic variants delly gatk rust-bio-tools snakemake-wrapper-utils tabix BCFtools BEDTools Bowtie 2 BWA Cutadapt FastQC fgbio FreeBayes mosdepth MultiQC Pandas Picard SAMtools Snakemake Variant Effect Predictor (VEP) vembrane numpy oschmod sklearn statsmodels Varlociraptor DNA
Free
127
varca
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Use an ensemble of variant callers to call variants from ATAC-seq data
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public

A pipeline for running an ensemble of variant callers to predict variants from ATAC-seq reads. The entire pipeline is made up...
VCF Data Variant calling genetic variants delly macs2 tabix BCFtools BEDTools BWA Pandas SAMtools Snakemake BBmisc data.table dplyr ggplot2 parallelMap plyr R.devices matplotlib numpy pysam sklearn ATAC-seq deep learning
Free
39
qadabra
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Snakemake workflow for comparison of differential abundance ranks
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public

Qadabra is a Snakemake workflow for running and comparing several differential abundance (DA) methods on the same microbiome ...
ANCOMBC Maaslin2 ALDEx2 Biobase biomformat DESeq2 edgeR metagenomeSeq Pandas phyloseq dplyr joblib matplotlib numpy seaborn sklearn UpSetPlot
Free
60
32vis
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Thirty-Two Years of IEEE VIS
public

public

This repository contains data files and codes (data processing & analysis) for the paper of Thirty-two years of IEEE VIS: Aut...
data JSON Pandas Snakemake bs4 numpy requests selenium sklearn urllib3
Free
44
charplant
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A de novo prediction tool of chromatin accessible regions for plant genomes
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public

The result of OCR (Open Chromatin Region) assay technologies such as DNase-seq and ATAC-seq represents the open state of a ti...
JSON macs2 BiocSklearn Bowtie 2 Snakemake keras matplotlib numpy pyfiglet sklearn
Free
15
atacseq_pipeline
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Ultimate ATAC-seq Data Processing & Analysis Pipeline
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public

From r A w (unaligned) BAM files to normali Z ed counts. A Snakemake implementation of the BSF's ATAC-seq Data ...
macs2 BEDTools Bowtie 2 Consensus DeepTools fastp homer MultiQC Pandas Pybedtools SAMBLASTER SAMtools Snakemake UROPA matplotlib numpy rpy2 scipy seaborn sklearn statsmodels umap
Free
37
dna-seq-benchmark
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A snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB), CHM (syndip) or other custom datasets
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A Snakemake workflow for benchmarking variant calling approaches with Genome in a Bottle (GIAB) data (and other custom benchm...
JSON Gene ID Variant calling genetic variants snakemake-wrapper-utils BCFtools BEDTools BWA mosdepth Pandas Picard RTG Core SAMtools Snakemake common numpy pysam scipy sklearn statsmodels Genomics
Free
48
rindti
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RINDTI: Simplifying Drug-Target Interaction Prediction with Protein Residue Interaction Networks
public

public

This repository aims to simplify the drug-target interaction prediction process which is based on protein residue interaction...
Target-Decoy Pandas RDKit Snakemake joblib numpy sklearn torch torch-geometric tqdm utils esm Protein interaction experiment
Free
20
icannolncrna-identification-classification-and-ann
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Automatic identification, classification and annotation of plant lncRNAs in transcriptomic sequences
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public

Introduction Installation Input Data Configuration Folders Running t...
gff2bed Biopython BioQC BLAST gffcompare Pandas Pybedtools Snakemake data.table dplyr ggplot2 ggpubr LncFinder purrr seqinr gtfparse matplotlib numpy scipy seaborn sklearn
Free
39
icannolncrna-identification-classification-and-ann
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Automatic identification, classification and annotation of plant lncRNAs in transcriptomic sequences
public

public

Introduction Installation Input Data Configuration Folders Running t...
gff2bed Biopython BioQC BLAST gffcompare Pandas Pybedtools Snakemake data.table dplyr ggplot2 ggpubr LncFinder purrr seqinr gtfparse matplotlib numpy scipy seaborn sklearn
Free
39
fprdg1
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Workflow for transcript expression analysis.
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public

In this workflow the abundances of transcipts are quantified using kallisto and analysed with sleuth. The resulting data ist ...
JSON biomaRt ComplexHeatmap gage kallisto Pandas pathview Pizzly Quant sleuth Snakemake calibrate circlize dplyr gridExtra MASS png rsvg h5py matplotlib numpy pysam seaborn sklearn
Free
25
paper
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Materials and Code for the micom manuscript.
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public

This repo includes workflows and additional data to reproduce the manuscript: MICOM: Metagenome-Scale Modeling To Infer Metab...
NG-Circos Pandas Snakemake ggplot2 adjustText joypy matplotlib micom mizani networkx numpy nxviz scikit-bio scipy seaborn sklearn
Free
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