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Revision: 15:fab6ff46e019

Repository 'seurat'

Clone this repository: hg clone https://toolshed.g2.bx.psu.edu/repos/iuc/seurat

Seurat tool metadata

Miscellaneous

Name: Seurat

Description: - toolkit for exploration of single-cell RNA-seq data

Id: seurat

Guid: toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat/4.3.0.1+galaxy1

Version: 4.3.0.1+galaxy1

Version command string: None

Display in tool panel: True

Version lineage of this tool (guids ordered most recent to oldest)

toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat/4.3.0.1+galaxy1 (this tool)

toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat/4.3.0+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat/4.2.0+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat/4.1.1+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat/4.1.0+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat/4.0.6+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat/4.0.5+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat/3.2.2+galaxy0

toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat/3.1.5+galaxy2

toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat/3.1.5+galaxy1

toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat/3.1.5

toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat/3.1.2

toolshed.g2.bx.psu.edu/repos/iuc/seurat/seurat/2.3.4

seurat

Requirements (dependencies defined in the <requirements> tag set)

Requirements:

name

version

type

r-seurat

4.3.0.1

package

r-rmarkdown

2.22

package

r-data.table

1.14.2

package

Functional tests

name

inputs

outputs

required files

Test-1

function|input: counts.tab.gz
function|min_cells: 3
function|min_genes: 200
function|low_thresholds: 1
function|high_thresholds: 20000000
function|vlnfeat: True
function|norm_file: True
function|variable_continue|featplot: True
function|variable_continue|var_file: True
function|variable_continue|pca_continue|pc_plots: True
function|variable_continue|pca_continue|pca_file: True
function|variable_continue|pca_continue|clusters_continue|resolution: 0.6
function|variable_continue|pca_continue|clusters_continue|nmds: True
function|variable_continue|pca_continue|clusters_continue|clusters_file: True
function|variable_continue|pca_continue|clusters_continue|markers_continue|min_pct: 0.25
function|variable_continue|pca_continue|clusters_continue|markers_continue|logfc_threshold: 0.25
function|variable_continue|pca_continue|clusters_continue|markers_continue|heatmaps: True
function|variable_continue|pca_continue|clusters_continue|markers_continue|markers_file: True
function|variable_continue|pca_continue|clusters_continue|markers_continue|markers_continue: yes
function|variable_continue|pca_continue|clusters_continue|clusters_continue: yes
function|variable_continue|pca_continue|pca_continue: yes
function|variable_continue|variable_continue: yes
function|function_select: base
meta|showcode: True
meta|warn: False
meta|varstate: False

name: value
name: value

counts.tab.gz
value

Test-2

function|input: counts.tab.gz
function|min_cells: 3
function|min_genes: 200
function|low_thresholds: 1
function|high_thresholds: 20000000
function|vlnfeat: True
function|norm_file: False
function|variable_continue|featplot: True
function|variable_continue|var_file: False
function|variable_continue|pca_continue|pc_plots: True
function|variable_continue|pca_continue|pca_file: False
function|variable_continue|pca_continue|clusters_continue|perplexity: 16
function|variable_continue|pca_continue|clusters_continue|resolution: 0.6
function|variable_continue|pca_continue|clusters_continue|nmds: True
function|variable_continue|pca_continue|clusters_continue|clusters_file: False
function|variable_continue|pca_continue|clusters_continue|markers_continue|min_pct: 0.25
function|variable_continue|pca_continue|clusters_continue|markers_continue|logfc_threshold: 0.25
function|variable_continue|pca_continue|clusters_continue|markers_continue|heatmaps: True
function|variable_continue|pca_continue|clusters_continue|markers_continue|markers_file: False
function|variable_continue|pca_continue|clusters_continue|markers_continue|markers_continue: yes
function|variable_continue|pca_continue|clusters_continue|clusters_continue: yes
function|variable_continue|pca_continue|pca_continue: yes
function|variable_continue|variable_continue: yes
function|function_select: base
meta|showcode: True
meta|warn: False
meta|varstate: False

name: value

counts.tab.gz
value

Test-3

function|rna: rna.tab.gz
function|prot: adt.tab.gz
function|min_cells: 0
function|min_genes: 0
function|low_thresholds: 1
function|high_thresholds: 20000000
function|vlnfeat: False
function|norm_file: False
function|featplot: True
function|var_file: False
function|num_PCs: 20
function|pc_plots: True
function|pca_file: False
function|resolution: 0.6
function|nmds: False
function|clusters_file: False
function|min_pct: 0.25
function|logfc_threshold: 0.25
function|heatmaps: True
function|markers_file: False
function|cite_markers: True
function|comparison|feat_comp: CD4,CD19
function|comparison|comparison: yes
function|marker_compare|top_x: 3
function|marker_compare|marker_compare: yes
function|function_select: cite
meta|showcode: True
meta|warn: False
meta|varstate: False

name: value
name: value

rna.tab.gz
adt.tab.gz
value

Test-4

function|rna: rna.tab.gz
function|prot: adt.tab.gz
function|min_cells: 0
function|min_genes: 0
function|low_thresholds: 1
function|high_thresholds: 20000000
function|vlnfeat: False
function|norm_file: True
function|featplot: True
function|var_file: True
function|num_PCs: 20
function|pc_plots: True
function|pca_file: True
function|resolution: 0.6
function|nmds: True
function|clusters_file: True
function|min_pct: 0.25
function|logfc_threshold: 0.25
function|heatmaps: True
function|markers_file: True
function|cite_markers: False
function|comparison|feat_comp: CD4,CD19
function|comparison|comparison: yes
function|marker_compare|top_x: 3
function|marker_compare|marker_compare: yes
function|function_select: cite
meta|showcode: True
meta|warn: False
meta|varstate: False

rna.tab.gz
adt.tab.gz