SCMCP

by huang-sh
Verified

Server Configuration

Describes the environment variables required to run the server.

NameRequiredDescriptionDefault

No arguments

Schema

Prompts

Interactive templates invoked by user choice

NameDescription

No prompts

Resources

Contextual data attached and managed by the client

NameDescription

No resources

Tools

Functions exposed to the LLM to take actions

NameDescription
read_h5ad

Read .h5ad-formatted hdf5 file

read_10x_h5

Read 10x-Genomics-formatted hdf5 file

read_10x_mtx

Read 10x-Genomics-formatted mtx directory.

read_text

Read gene expression from .txt, .csv, .tsv file.

write

Write AnnData objects to file.

filter_genes

Filter genes based on number of cells or counts

filter_cells

Filter cells based on counts and numbers of genes expressed.

calculate_qc_metrics

Calculate quality control metrics(common metrics: total counts, gene number, percentage of counts in ribosomal and mitochondrial) for AnnData.

log1p

Logarithmize the data matrix (X = log(X + 1))

normalize_total

Normalize counts per cell to the same total count

pca

Principal component analysis

highly_variable_genes

Annotate highly variable genes

regress_out

Regress out (mostly) unwanted sources of variation.

scale

Scale data to unit variance and zero mean

combat

ComBat function for batch effect correction

scrublet

Predict doublets using Scrublet

neighbors

Compute nearest neighbors distance matrix and neighborhood graph

tsne

t-distributed stochastic neighborhood embedding (t-SNE), for visualizating single-cell data

umap

Uniform Manifold Approximation and Projection (UMAP) for visualization

draw_graph

Force-directed graph drawing for visualization

diffmap

Diffusion Maps for dimensionality reduction

embedding_density

Calculate the density of cells in an embedding

leiden

Leiden clustering algorithm for community detection

louvain

Louvain clustering algorithm for community detection

dendrogram

Hierarchical clustering dendrogram

dpt

Diffusion Pseudotime (DPT) analysis

paga

Partition-based graph abstraction

ingest

Map labels and embeddings from reference data to new data

rank_genes_groups

Rank genes for characterizing groups, perform differentially expressison analysis

filter_rank_genes_groups

Filter out genes based on fold change and fraction of genes

marker_gene_overlap

Calculate overlap between data-derived marker genes and reference markers

score_genes

Score a set of genes based on their average expression

score_genes_cell_cycle

Score cell cycle genes and assign cell cycle phases

pl_pca

Scatter plot in PCA coordinates. default figure for PCA plot

pl_embedding

Scatter plot for user specified embedding basis (e.g. umap, tsne, etc).

pl_violin

Plot violin plot of one or more variables.

pl_stacked_violin

Plot stacked violin plots. Makes a compact image composed of individual violin plots stacked on top of each other.

pl_heatmap

Heatmap of the expression values of genes.

pl_dotplot

Plot dot plot of expression values per gene for each group.

pl_matrixplot

matrixplot, Create a heatmap of the mean expression values per group of each var_names.

pl_tracksplot

tracksplot,compact plot of expression of a list of genes..

pl_scatter

Plot a scatter plot of two variables, Scatter plot along observations or variables axes.

pl_rank_genes_groups_dotplot

Plot ranking of genes(DEGs) using dotplot visualization. Defualt plot DEGs for rank_genes_groups tool

pl_highly_variable_genes

plot highly variable genes; Plot dispersions or normalized variance versus means for genes.

pl_pca_variance_ratio

Plot the PCA variance ratio to visualize explained variance.

mark_var

Determine if each gene meets specific conditions and store results in adata.var as boolean values.for example: mitochondrion genes startswith MT-.the tool should be call first when calculate quality control metrics for mitochondrion, ribosomal, harhemoglobin genes. or other qc_vars

list_var

list key columns in adata.var. it should be called for checking when other tools need var key column names input

list_obs

List key columns in adata.obs. It should be called before other tools need obs key column names input

check_gene

Check if genes exist in adata.var_names. This tool should be called before gene expression visualizations or color by genes.

ls_ccc_method

List cell-cell communication method.

ccc_rank_aggregate

Get an aggregate of ligand-receptor scores from multiple Cell-cell communication methods.

ccc_circle_plot

Visualize cell-cell communication network using a circular plot.

ccc_dot_plot

Visualize cell-cell communication interactions using a dotplot.

ccc

Cell-cell communication analysis with one method (cellphonedb, cellchat,connectome, natmi, etc.)

ID: hqyo2icqci