Workflows

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161 Workflows visible to you, out of a total of 161
gcms-metams/main

This workflow is composed with the XCMS tool R package (Smith, C.A. 2006) able to extract and the metaMS R package (Wehrens, R 2014) for the field of untargeted metabolomics.

https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/gcms/tutorial.html

Type: Galaxy

Creator: workflow4metabolomics

Submitter: WorkflowHub Bot

gromacs-mmgbsa/main

MMGBSA simulation and calculation

Type: Galaxy

Creators: Simon Bray, Simon Bray

Submitter: WorkflowHub Bot

lcms-preprocessing/main

This workflow is composed with the XCMS tool R package (Smith, C.A. 2006) able to extract, filter, align and fill gapand the possibility to annotate isotopes, adducts and fragments using the CAMERA R package (Kuhl, C 2012).

https://training.galaxyproject.org/training-material/topics/metabolomics/tutorials/lcms-preprocessing/tutorial.html

Type: Galaxy

Creator: workflow4metabolomics

Submitter: WorkflowHub Bot

Assembly-Hifi-HiC-phasing-VGP4/main

Contiging Solo w/HiC:

Generate phased assembly based on PacBio Hifi Reads using HiC data from the same individual for phasing.

Inputs

  1. Hifi long reads [fastq]
  2. HiC forward reads (if multiple input files, concatenated in same order as reverse reads) [fastq]
  3. HiC reverse reads (if multiple input files, concatenated in same order as forward reads) [fastq]
  4. K-mer database [meryldb]
  5. Genome profile summary generated by Genomescope [txt]
  6. Name of first assembly
  7. Name of second assembly ...

Type: Galaxy

Creators: Delphine Lariviere, Galaxy, VGP

Submitter: WorkflowHub Bot

sra-manifest-to-concatenated-fastqs/main

This workflow takes as input a SRA_manifest from SRA Run Selector and will generate one fastq file or fastq pair of file for each experiment (concatenated multiple runs if necessary). Output will be relabelled to match the column specified by the user.

Type: Galaxy

Creators: Lucille Delisle, Pierre Osteil, Wolfgang Maier

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

repeatmasking/main

RepeatMasking Workflow

This workflow uses RepeatModeler and RepeatMasker for genome analysis.

  • RepeatModeler is a software package for identifying and modeling de novo families of transposable elements (TEs). At the heart of RepeatModeler are three de novo repeat search programs (RECON, RepeatScout and LtrHarvest/Ltr_retriever) which use complementary computational methods to identify repeat element boundaries and family relationships from sequence data.

  • RepeatMasker is a program that analyzes ...

Type: Galaxy

Creator: Romane Libouban

Submitter: WorkflowHub Bot

polish-with-long-reads/main

Racon polish with long reads, x4

Type: Galaxy

Creator: Anna Syme

Submitter: WorkflowHub Bot

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