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Update cross_server_tools.md
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description of new transcriptomics functions
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Clare72 authored Sep 18, 2023
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Expand Up @@ -53,7 +53,7 @@ Classes
`classification = 'class expression' e.g. "'Kenyon cell'" or "'neuron' that overlaps 'lateral horn'".

`get_neurons_upstream_of(self, neuron, weight, classification=None, query_by_label=True, return_dataframe=True)`
: Get all neurons downstream of individual `neuron` (short_form if query_by_label=False, otherwise label)
: Get all neurons upstream of individual `neuron` (short_form if query_by_label=False, otherwise label)
with connection strength > threshold. Optionally restrict target neurons to those specified by
`classification = 'class expression' e.g. "'Kenyon cell'" or "'neuron' that overlaps 'lateral horn'".

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`get_vfb_link(self, short_forms: <built-in function iter>, template)`
: Takes a list of VFB IDs (short_forms) and the name (label) of a template.
Returns a link to VFB loading all available images
of neurons on that template.
of neurons on that template.

`get_gene_function_filters(self)`
: Returns a list of all unique gene function labels in the database in alphabetical order.

`get_transcriptomic_profile(self, cell_type, gene_type=False, return_dataframe=True)`
: Takes a cell_type (name, ID or symbol) from the Drosophila anatomy ontology as a String.
Returns transcriptomics data for clusters annotated as the given cell_type (and subtypes).
Can optionally be restricted to genes of a particular function by specifying gene_type as a String.
Available gene functions can be retrieved by running get_gene_function_filters().

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