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comparison scanpy-neighbours.xml @ 28:6417cccad133 draft

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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 6c9d530aa653101e9e21804393ec11f38cddf027-dirty
author ebi-gxa
date Thu, 16 Feb 2023 13:29:23 +0000
parents fcaa9048cdaf
children f776e3ed3c03
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27:a58d4166805b 28:6417cccad133
1 <?xml version="1.0" encoding="utf-8"?> 1 <?xml version="1.0" encoding="utf-8"?>
2 <tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy0" profile="@PROFILE@"> 2 <tool id="scanpy_compute_graph" name="Scanpy ComputeGraph" version="@TOOL_VERSION@+galaxy9" profile="@PROFILE@">
3 <description>to derive kNN graph</description> 3 <description>to derive kNN graph</description>
4 <macros> 4 <macros>
5 <import>scanpy_macros2.xml</import> 5 <import>scanpy_macros2.xml</import>
6 </macros> 6 </macros>
7 <expand macro="requirements"/> 7 <expand macro="requirements"/>
130 Compute a neighborhood graph of observations (`pp.neighbors`) 130 Compute a neighborhood graph of observations (`pp.neighbors`)
131 ============================================================= 131 =============================================================
132 132
133 The neighbor search efficiency of this heavily relies on UMAP (McInnes et al, 2018), 133 The neighbor search efficiency of this heavily relies on UMAP (McInnes et al, 2018),
134 which also provides a method for estimating connectivities of data points - 134 which also provides a method for estimating connectivities of data points -
135 the connectivity of the manifold (`method=='umap'`). If `method=='diffmap'`, 135 the connectivity of the manifold (`method=='umap'`). If `method=='Gaussian'`,
136 connectivities are computed according to Coifman et al (2005), in the adaption of 136 connectivities are computed according to Coifman et al (2005), in the adaption of
137 Haghverdi et al (2016). 137 Haghverdi et al (2016).
138 138
139 @HELP@ 139 @HELP@
140 140