annotate/celltypist

Description

Automated cell type annotation tool for scRNA-seq datasets on the basis of logistic regression classifiers optimised by the stochastic gradient descent algorithm.

Inputs

Name	Type & Properties	Description
--input -i	file required	The input (query) data to be labeled. Should be a .h5mu file.
--modality	string	Which modality to process.
--input_layer	string	The layer in the input data containing log normalized counts to be used for cell type annotation if .X is not to be used.
--input_var_gene_names	string	The name of the adata var column in the input data containing gene names; when no gene_name_layer is provided, the var index will be used.
--input_reference_gene_overlap	integer	The minimum number of genes present in both the reference and query datasets.

Name

Type & Properties

--input

-i

file

required

--modality

string

--input_layer

string

--input_var_gene_names

string

--input_reference_gene_overlap

integer

Reference

Name	Type & Properties	Description
--reference	file	The reference data to train the CellTypist classifiers on. Only required if a pre-trained --model is not provided.
--reference_layer	string	The layer in the reference data to be used for cell type annotation if .X is not to be used. Data are expected to be processed in the same way as the --input query dataset.
--reference_obs_target	string	The name of the adata obs column in the reference data containing cell type annotations.
--reference_var_gene_names	string	The name of the adata var column in the reference data containing gene names; when no gene_name_layer is provided, the var index will be used.
--reference_var_input	string	.var column containing highly variable genes. By default, do not subset genes.

Name

Type & Properties

--reference

file

--reference_layer

string

--reference_obs_target

string

--reference_var_gene_names

string

--reference_var_input

string

Model arguments

Name	Type & Properties	Description
--model	file	Pretrained model in pkl format. If not provided, the model will be trained on the reference data and --reference should be provided.
--feature_selection	boolean	Whether to perform feature selection.
--majority_voting	boolean	Whether to refine the predicted labels by running the majority voting classifier after over-clustering.
--C	double	Inverse of regularization strength in logistic regression.
--max_iter	integer	Maximum number of iterations before reaching the minimum of the cost function.
--use_SGD	boolean_true	Whether to use the stochastic gradient descent algorithm.
--min_prop	double	"For the dominant cell type within a subcluster, the minimum proportion of cells required to support naming of the subcluster by this cell type. Ignored if majority_voting is set to False. Subcluster that fails to pass this proportion threshold will be assigned 'Heterogeneous'."

Name

Type & Properties

--model

file

--feature_selection

boolean

--majority_voting

boolean

--C

double

--max_iter

integer

--use_SGD

boolean_true

--min_prop

double

Outputs

Name	Type & Properties	Description
--output	file output	Output h5mu file.
--output_obs_predictions	string	In which `.obs` slots to store the predicted information.
--output_obs_probability	string	In which `.obs` slots to store the probability of the predictions.
--output_compression	string	Compression format to use for the output AnnData and/or Mudata objects. By default no compression is applied.

Name

Type & Properties

--output

file

output

--output_obs_predictions

string

--output_obs_probability

string

--output_compression

string

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
modality: [ "rna" ]  
input_reference_gene_overlap: [ 100 ]  
reference_obs_target: [ "cell_ontology_class" ]  
feature_selection: [ false ]  
majority_voting: [ false ]  
C: [ 1 ]  
max_iter: [ 1000 ]  
min_prop: [ 0 ]  
output: "$id.$key.output.h5mu"  
output_obs_predictions: [ "celltypist_pred" ]  
output_obs_probability: [ "celltypist_probability" ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v3.0.0 \  
  -main-script target/nextflow/annotate/celltypist/main.nf \  
  -params-file params.yaml

annotate/celltypist

Inputs

Reference

Model arguments

Outputs

Run this component

Relationships

Used by

Uses