Workflows

What is a Workflow?
180 Workflows visible to you, out of a total of 180
fluorescence-nuclei-segmentation-and-counting/main

This workflow performs segmentation and counting of cell nuclei using fluorescence microscopy images. The segmentation step is performed using Otsu thresholding (Otsu, 1979). The workflow is based on the tutorial: https://training.galaxyproject.org/training-material/topics/imaging/tutorials/imaging-introduction/tutorial.html

Type: Galaxy

Creator: Leonid Kostrykin

Submitter: WorkflowHub Bot

assembly-with-flye/main

Assemble long reads with Flye, then view assembly statistics and assembly graph

Type: Galaxy

Creator: Anna Syme

Submitter: WorkflowHub Bot

velocyto/Velocyto-on10X-from-bundled

Run velocyto to get loom with counts of spliced and unspliced. It will extract the 'barcodes' from the bundled outputs.

Type: Galaxy

Creator: Lucille Delisle

Submitter: WorkflowHub Bot

gromacs-mmgbsa/main

MMGBSA simulation and calculation

Type: Galaxy

Creators: Simon Bray, Simon Bray

Submitter: WorkflowHub Bot

baredsc/baredSC-1d-logNorm

Run baredSC in 1 dimension in logNorm for 1 to N gaussians and combine models.

Type: Galaxy

Creator: Lucille Delisle

Submitter: WorkflowHub Bot

openms-metaprosip/main

Automated inference of stable isotope incorporation rates in proteins for functional metaproteomics

Type: Galaxy

Creator: Matthias Bernt

Submitter: WorkflowHub Bot

average-bigwig-between-replicates/main

We assume the identifiers of the input list are like: sample_name_replicateID. The identifiers of the output list will be: sample_name

Type: Galaxy

Creator: Lucille Delisle

Submitter: WorkflowHub Bot

polish-with-long-reads/main

Racon polish with long reads, x4

Type: Galaxy

Creator: Anna Syme

Submitter: WorkflowHub Bot

parallel-accession-download/main

Downloads fastq files for sequencing run accessions provided in a text file using fasterq-dump. Creates one job per listed run accession.

Type: Galaxy

Creators: Marius van den Beek, IWC

Submitter: WorkflowHub Bot

consensus-peaks/consensus-peaks-chip-sr

This workflow takes as input SR BAM from ChIP-seq. It calls peaks on each replicate and intersect them. In parallel, each BAM is subsetted to smallest number of reads. Peaks are called using both subsets combined. Only peaks called using a combination of both subsets which have summits intersecting the intersection of both replicates will be kept.

Type: Galaxy

Creator: Lucille Delisle

Submitter: WorkflowHub Bot

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