pseudobulk-worflow-decoupler-edger/main

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Workflow Type: Galaxy

This workflow uses the decoupler tool in Galaxy to generate pseudobulk counts from an annotated AnnData file obtained from scRNA-seq analysis. Following the pseudobulk step, differential expression genes (DEG) are calculated using the edgeR tool. The workflow also includes data sanitation steps to ensure smooth operation of edgeR and minimizing potential issues. Additionally, a Volcano plot tool is used to visualize the results after the DEG analysis.

SEEK ID: https://workflowhub.eu/workflows/1207?version=2

Inputs

ID Name Description Type
Factor fields Factor fields The fields from Obs to be provided to EdgeR as factors. The first field should represent the main contrast for comparisons, while the subsequent fields will be used as covariates.
  • string
Formula Formula Example 1: ~ 0 + Factor_1 (Use this formula when you only want to account for one factor, Factor_1). Example 2 (With covariate adjustment): ~ 0 + Factor_1 + Factor_2 (Use this formula if you need to adjust for additional factors, such as Factor_2, which serves as a covariate). Note: Ensure that all factors (e.g., Factor_1, Factor_2) included in the formula are defined in your factor file.
  • string
Gene symbol column Gene symbol column Specify the name of the column containing your gene symbols. For example: gene_symbol, gene_name, x, etc.
  • string
Group by column Group by column Typically, the column in obs that you want to use for comparisons later (the main contrast field) should be specified here. This column will also be used for plotting the pseudo-bulk samples, showing the number of counts and cells.
  • string
Name Your Raw Counts Layer Name Your Raw Counts Layer Name of the layer containing your raw (non-normalized) counts.
  • string
Pseudo-bulk: Fields to merge Pseudo-bulk: Fields to merge Merge Obs fields before pseudo-bulk analysis to create new categories for grouping, such as 'sample,phase' or 'sample,louvain'. Ensure the fields exist in the Obs of the AnnData object. Multiple groups can be merged with a colon (':'), e.g., 'sample,phase ,phase' creates 'sample_phase' and 'louvain_phase'.
  • string?
Sample key column Sample key column The field used to create the pseudo-bulk replicates is typically a combination of multiple Obs fields merged together.
  • string
Source AnnData file Source AnnData file Ensure your AnnData object contains all necessary layers before using the decoupler tool. The raw counts should be included in AnnData. If they are missing, create a new layer (e.g., 'raw_counts') and copy the raw counts into it.
  • File

Steps

ID Name Description
8 Decoupler pseudo-bulk toolshed.g2.bx.psu.edu/repos/ebi-gxa/decoupler_pseudobulk/decoupler_pseudobulk/1.4.0+galaxy8
9 Sanitize matrix toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1
10 Sanitize factors toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1
11 Remove start, end, width A column that may affect EdgeR and DESeq2. toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0
12 Sanitize first factor for leading digits toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_column/9.3+galaxy1
13 Text reformatting toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_awk_tool/9.3+galaxy1
14 edgeR toolshed.g2.bx.psu.edu/repos/iuc/edger/edger/3.36.0+galaxy5
15 Get contrast labels toolshed.g2.bx.psu.edu/repos/iuc/collection_element_identifiers/collection_element_identifiers/0.0.2
16 Select gene symbols, logFC, PValue and FDR toolshed.g2.bx.psu.edu/repos/iuc/column_remove_by_header/column_remove_by_header/1.0
17 Replace Text toolshed.g2.bx.psu.edu/repos/bgruening/text_processing/tp_replace_in_line/9.3+galaxy1
18 Split contrasts toolshed.g2.bx.psu.edu/repos/bgruening/split_file_to_collection/split_file_to_collection/0.5.2
19 Contrast as parameters param_value_from_file
20 Volcano Plot toolshed.g2.bx.psu.edu/repos/iuc/volcanoplot/volcanoplot/0.0.6

Outputs

ID Name Description Type
Pseudobulk count matrix Pseudobulk count matrix n/a
  • File
Pseudobulk Plot Pseudobulk Plot n/a
  • File
Filtered by expression Filtered by expression n/a
  • File
Tables: DEG Tables: DEG n/a
  • File
Report Results: HTML File Report Results: HTML File n/a
  • File
Tables for volcano plot Tables for volcano plot n/a
  • File
Volcano Plot on input dataset(s): PDF Volcano Plot on input dataset(s): PDF n/a
  • File

Version History

v0.1.1 (latest) Created 22nd Nov 2024 at 03:02 by WorkflowHub Bot

Updated to v0.1.1


Frozen v0.1.1 1a15aa4

v0.1 (earliest) Created 17th Nov 2024 at 03:03 by WorkflowHub Bot

Updated to v0.1


Frozen v0.1 72f8bbd
help Creators and Submitter
Creators
  • Diana Chiang Jurado
  • Pavankumar Videm
  • Pablo Moreno
Submitter
Tool
edgeR
License
Creative Commons Attribution 4.0 International
Activity

Views: 44   Downloads: 12   Runs: 0

Created: 17th Nov 2024 at 03:03

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