Preprocessing: pp¶
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Adds prefix to the headers/contig ids in cellranger fasta and annotation file. |
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Adds prefix to the headers/contig ids in cellranger fasta and annotation file. |
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Annotate contigs with constant region call using blastn |
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Annotate contigs with constant region call using blastn |
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Reannotate cellranger fasta files with igblastn and parses to airr/changeo data format. |
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Correct allele calls based on a personalized genotype using tigger-reassignAlleles. |
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Runs CreateGermlines.py to reconstruct the germline V(D)J sequence, from which the Ig lineage and mutations can be inferred. |
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Filters doublets and poor quality cells and corresponding contigs based on provided V(D)J DataFrame and AnnData objects. |
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Runs basic mutation load analysis implemented in shazam. |
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Calculating nearest neighbor distances for tuning clonal assignment with shazam. |
Preprocessing (external): pp.external¶
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Reannotate with IgBLASTn. |
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Parses IgBLAST output to airr format. |
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Parses AIRR table (heavy chain contigs only). |
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Parses AIRR table (light chain contigs only). |
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Parses AIRR table (light chain contigs only). |
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Wrapper for CreateGermlines.py for reconstructing germline sequences, |
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Reassign alleles with TIgGER in R. |
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Recipe for running a standard scanpy QC workflow. |
Tools: tl¶
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Find clones based on heavy chain and light chain CDR3 junction hamming distance. |
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Find clones using changeo’s DefineClones.py. |
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Quantifies size of clones |
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A function to tabulate clonal overlap for input as a circos-style plot. :Parameters: * self (Dandelion, AnnData) – Dandelion or AnnData object. * groupby (str) – column name in obs/metadata for collapsing to nodes in circos plot. * colorby (str) – column name in obs/metadata for grouping and color of nodes in circos plot. * min_clone_size (int, optional) – minimum size of clone for plotting connections. Defaults to 2 if left as None. * clone_key (str, optional) – column name for clones. None defaults to ‘clone_id’. |
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Transfer data in Dandelion slots to AnnData object, updating the .obs, .uns, .obsm and `.obsp`slots. |
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Generates a Levenshtein distance network based on full length VDJ sequence alignments for heavy and light chain(s). |
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Calculates node degree in BCR network. |
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Calculates node closeness centrality in BCR network. |
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Retrieves edge weights (BCR levenshtein distance) from graph. |
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Compute B cell clones diversity : Gini indices, Chao1 estimates, or Shannon entropy. |
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Returns rarefaction predictions for cell numbers vs clone size. :Parameters: * self (Dandelion, AnnData) – Dandelion or AnnData object. * groupby (str) – Column name to split the calculation of clone numbers for a given number of cells for e.g. sample, patient etc. * clone_key (str, optional) – Column name specifying the clone_id column in metadata/obs. * diversity_key (str, optional) – key for ‘diversity’ results in AnnData’s .uns. |
Plotting: pl¶
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Plots rarefaction curve for cell numbers vs clone size. |
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Using scanpy’s plotting module to plot the network. |
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A barplot function to plot usage of V/J genes in the data. |
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A stackedbarplot function to plot usage of V/J genes in the data split by groups. |
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A stackedbarplot function to plot usage of V/J genes in the data split by groups. |
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A plot function to visualise clonal overlap as a circos-style plot. |
Utilities: utl¶
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Runs makeblastdb. |
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Reads in or copy dataframe object and set sequence_id as index without dropping. |
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Dandelion class object. |
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A Dandelion function to update and populate the .metadata slot. |
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Reads in and returns a Dandelion class from .h5 format. |
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Reads in and returns a Dandelion class saved using pickle format. |