An analysis pipeline for patch seq data, a combination of patch-clamp electrophysiology and single cell sequencing. The data is not yet publicly available.
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ephys_feature_extraction.py
Calculates electrophysiological features from raw recordings. Since this is the only script that loads raw recordings, it also generates example figures. The features are saved as ephys_features_df.csv
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ephys_annotation.py
Annotates the electrophysiological features with metadata and coordinates of a t-SNE embedding. This script also clusters samples into putative pyramidal cells and interneurons based on their electrophysiological properties. Output is ephys_features_annotated_df.csv
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transcriptomics_quality_control.py
Quality control on samples and genes using scanpy package. Also normalizes read counts to Log2 counts-per-million and annotates metadata. Output is count_exons_introns_full_named_postqc.h5ad
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combine_transcriptomics_ephys.py
Annotate electrophysiological with transcriptomic data and vice-versa. The output must be two data structures because not all recorded samples were sequenced and missing rows must be avoided in scanpy's annotated dataframe. Outputs are ephys_full_df.csv and trans_anndf.h5ad
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stats_ephys_transgenic_type.py
Statistically tests whether transgenically defined interneuron types are significantly different regarding their electrophysiological features. Does not implement multiple comparison correction yet.
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stats_transcriptomic_type_ephys.py
Statistically tests whether transcriptomically defined interneuron types are significantly differen regarding their electrophysiological features. Transcriptomic cell types are defined by their CPM. Does not implement multiple comparison correction yet.
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stats_differential_expression.py
Differential expression analysis to identify marker genes of a specific transcriptomic cell type.