Mercurial > repos > iuc > scanpy_inspect

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/scanpy/ commit 9d49b2a98de059ae9a053dc1c5a23537cf0311de
author iuc
date Sat, 18 May 2024 18:33:09 +0000
parents 3081ff5c84a3
children
comparison
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13:5c3ebe2adc77 14:f54f0f0598ad
891 - mean_{expr_type} (e.g. "mean counts", mean expression over all cells) 891 - mean_{expr_type} (e.g. "mean counts", mean expression over all cells)
892 - n_cells_by_{expr_type} (e.g. "n_cells_by_counts", number of cells this expression is measured in) 892 - n_cells_by_{expr_type} (e.g. "n_cells_by_counts", number of cells this expression is measured in)
893 - pct_dropout_by_{expr_type} (e.g. "pct_dropout_by_counts", percentage of cells this feature does not appear in) 893 - pct_dropout_by_{expr_type} (e.g. "pct_dropout_by_counts", percentage of cells this feature does not appear in)
894 894
895 More details on the `scanpy documentation 895 More details on the `scanpy documentation
896 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.calculate_qc_metrics.html>`__ 896 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.calculate_qc_metrics.html>`__
897 897
898 Compute a neighborhood graph of observations, using `pp.neighbors` 898 Compute a neighborhood graph of observations, using `pp.neighbors`
899 ================================================================== 899 ==================================================================
900 900
901 The neighbor search efficiency of this heavily relies on UMAP (McInnes et al, 2018), 901 The neighbor search efficiency of this heavily relies on UMAP (McInnes et al, 2018),
910 - Distances for each pair of neighbors (distances) 910 - Distances for each pair of neighbors (distances)
911 911
912 This data are stored in the unstructured annotation (uns) and can be accessed using the inspect tool for AnnData objects 912 This data are stored in the unstructured annotation (uns) and can be accessed using the inspect tool for AnnData objects
913 913
914 More details on the `scanpy documentation 914 More details on the `scanpy documentation
915 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.neighbors.html>`__ 915 <https://scanpy.readthedocs.io/en/stable/api/generated/scanpy.pp.neighbors.html>`__
916 916
917 Score a set of genes, using `tl.score_genes` 917 Score a set of genes, using `tl.score_genes`
918 ============================================ 918 ============================================
919 919
920 The score is the average expression of a set of genes subtracted with the 920 The score is the average expression of a set of genes subtracted with the
923 923
924 This reproduces the approach in Seurat (Satija et al, 2015) and has been implemented 924 This reproduces the approach in Seurat (Satija et al, 2015) and has been implemented
925 for Scanpy by Davide Cittaro. 925 for Scanpy by Davide Cittaro.
926 926
927 More details on the `scanpy documentation 927 More details on the `scanpy documentation
928 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.score_genes.html>`__ 928 <https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.score_genes.html>`__
929 929
930 Score cell cycle genes, using `tl.score_genes_cell_cycle` 930 Score cell cycle genes, using `tl.score_genes_cell_cycle`
931 ========================================================= 931 =========================================================
932 932
933 Given two lists of genes associated to S phase and G2M phase, calculates 933 Given two lists of genes associated to S phase and G2M phase, calculates
934 scores and assigns a cell cycle phase (G1, S or G2M). See 934 scores and assigns a cell cycle phase (G1, S or G2M). See
935 `score_genes` for more explanation. 935 `score_genes` for more explanation.
936 936
937 More details on the `scanpy documentation 937 More details on the `scanpy documentation
938 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.score_genes_cell_cycle.html>`__ 938 <https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.score_genes_cell_cycle.html>`__
939 939
940 Rank genes for characterizing groups, using `tl.rank_genes_groups` 940 Rank genes for characterizing groups, using `tl.rank_genes_groups`
941 ================================================================== 941 ==================================================================
942 942
943 The returned AnnData object contains: 943 The returned AnnData object contains:
949 - Ajusted p-values 949 - Ajusted p-values
950 950
951 This data are stored in the unstructured annotation (uns) and can be accessed using the inspect tool for AnnData objects 951 This data are stored in the unstructured annotation (uns) and can be accessed using the inspect tool for AnnData objects
952 952
953 More details on the `scanpy documentation 953 More details on the `scanpy documentation
954 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.tl.rank_genes_groups.html>`__ 954 <https://scanpy.readthedocs.io/en/stable/api/scanpy.tl.rank_genes_groups.html>`__
955 955
956 956
957 Calculate an overlap score between data-deriven marker genes and provided markers (`tl.marker_gene_overlap`) 957 Calculate an overlap score between data-deriven marker genes and provided markers (`tl.marker_gene_overlap`)
958 ============================================================================================================ 958 ============================================================================================================
959 959
962 962
963 Logarithmize the data matrix (`pp.log1p`) 963 Logarithmize the data matrix (`pp.log1p`)
964 ========================================= 964 =========================================
965 965
966 More details on the `scanpy documentation 966 More details on the `scanpy documentation
967 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.log1p.html>`__ 967 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.log1p.html>`__
968 968
969 Scale data to unit variance and zero mean (`pp.scale`) 969 Scale data to unit variance and zero mean (`pp.scale`)
970 ====================================================== 970 ======================================================
971 971
972 More details on the `scanpy documentation 972 More details on the `scanpy documentation
973 <https://icb-scanpy.readthedocs-hosted.com/en/stable/api/scanpy.pp.scale.html>`__ 973 <https://scanpy.readthedocs.io/en/stable/api/scanpy.pp.scale.html>`__
974 974
975 Computes the square root the data matrix (`pp.sqrt`) 975 Computes the square root the data matrix (`pp.sqrt`)
976 ==================================================== 976 ====================================================
977 977
978 `X = sqrt(X)` 978 `X = sqrt(X)`