Mercurial > repos > ebi-gxa > scanpy_multiplet_scrublet

comparison scanpy-multiplet-scrublet.xml @ 8:53ce0e336840 draft default tip

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planemo upload for repository https://github.com/ebi-gene-expression-group/container-galaxy-sc-tertiary/tree/develop/tools/tertiary-analysis/scanpy commit 1161fdc6d874689d9a7a10bbe22b7758b2edc4bf-dirty
author ebi-gxa
date Wed, 15 May 2024 09:40:10 +0000
parents 2f9517a24c73
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7:2f9517a24c73 8:53ce0e336840
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113 **What it does** 113 **What it does**
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115 Predict cell doublets using a nearest-neighbor classifier of observed transcriptomes and simulated doublets. Works best if the input is a raw (unnormalized) counts matrix from a single sample or a collection of similar samples from the same experiment. This function is a wrapper around functions that pre-process using Scanpy and directly call functions of Scrublet(). 115 Predict cell doublets using a nearest-neighbor classifier of observed transcriptomes and simulated doublets. Works best if the input is a raw (unnormalized) counts matrix from a single sample or a collection of similar samples from the same experiment. This function is a wrapper around functions that pre-process using Scanpy and directly call functions of Scrublet().
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117 This is a wrapper around the Scanpy wrapper for Scrublet- see https://scanpy.readthedocs.io/en/stable/generated/scanpy.external.pp.scrublet.html. 117 This is a wrapper around the Scanpy wrapper for Scrublet- see https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pp.scrublet.html.
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119 **Note** 119 **Note**
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121 Where a threshold is not provided, Scrublet will try to automatically set one based on simulations, but this does not always work. There will be a warning, and no 'threshold' slot will be populated in .uns['scrublet']. The 'predicted_doublets' slot in .obs will be set to False for all cells such that no filtering will occur if this column is supplied to filtering steps. You can use the 'Scanpy Plot Scrublet' tool to plot the distribution of scores yourself and estimate a threshold to override this behaviour. 121 Where a threshold is not provided, Scrublet will try to automatically set one based on simulations, but this does not always work. There will be a warning, and no 'threshold' slot will be populated in .uns['scrublet']. The 'predicted_doublets' slot in .obs will be set to False for all cells such that no filtering will occur if this column is supplied to filtering steps. You can use the 'Scanpy Plot Scrublet' tool to plot the distribution of scores yourself and estimate a threshold to override this behaviour.
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