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scGEAToolbox (single-cell Gene Expression Analysis Toolbox)
Version 24.7.7 (254 MB) by
James Cai
Single-cell Gene Expression Analysis Toolbox
Share 'scGEAToolbox (single-cell Gene Expression Analysis Toolbox)'
Cite As
Cai JJ. scGEAToolbox: a Matlab toolbox for single-cell RNA sequencing data analysis. Bioinformatics. 2019 Nov 7:btz830. doi: 10.1093/bioinformatics/btz830. PMID: 31697351.
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- cdgea
- demo_Getting_Started.m
- online_landing.m
- scgeatool
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- sc_cellscore_admdl
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- i_species2taxid
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- main_centers.m
- main_citeseq.m
- nearest_neighbors_classifier
- plot_data.m
- scGeneFit
- scGeneFit_centers
- select_center_constraints
- select_constraints.m
- significant_cluster.m
- sqz_hinge
- subcluster_by_label
- subsample.m
+run/external/ml_scGeneFit/source/classification_metrics
+run/external/py_SERGIO
+run/external/py_harmonypy
+run/external/py_writeh5ad
+run/external/web_STRING/stringdb
+run/private
+run/thirdparty/MPPC
- addPoints
- calculateEnergy
- checkSingletons
- computeProjs
- connectCompsE
- energyCut
- getUnifPoints
- initialize
- modifySpacingAllComps
- mppc
- numPointsAdd
- plotADP
- removePoints
- remZeroMassPoints
- runex
- tridiag
- updateyzb
+run/thirdparty/alona_panglaodb
- i1_preparemarkerdb.m
- i2_markergeneweight.m
- i2_markergeneweight_dr_zebrafish.m
- i_makeuniquename
- sc_celltypes_slow
+run/thirdparty/alona_panglaodb/msigdb_c8
+run/thirdparty/alona_subtypes
+run/thirdparty/k-NN-code
- estim_beta_k_NN.m
- i_graph2graph.m
- knn_distmat
- knn_graph_estim_1
- knn_graph_estim_2
- L2_distance
- plot_knn
- swiss_roll_example.m
+run/thirdparty/locfit/Source
+run/thirdparty/locfit/m
- aic
- aicplot
- backtr
- fitted
- gcv
- gcvplot
- hatmatrix
- invlink
- kappa0
- lcv
- lcvplot
- lfband
- lfgui
- lfknots
- lfmarg
- lfplot
- lfsmooth
- lf_censor
- locfit
- locfit_all
- plotbyfactor
- predict
- residuals
- rsum
- scb
- smooth_lf
- spence15
- spence21
- test_smooth_locfit.m
- vecr
+ten
- apcluster.m
- check_tensor_toolbox
- compute_kernel
- do_td_cp
- do_td_tucker
- e_apcluster
- e_fgseanet
- e_fgsearun
- e_filtadjc
- e_mashup
- e_mkqqplot
- e_modlcomp
- e_prunenet
- Helper
- i_dr
- i_knk
- i_ma
- i_nc
- i_nct
- i_td1
- i_td2
- knk1_makeRefNetwork
- knk2_knockoutTargetGene
- knk3_buildPerturbationLandscape
- knk4_buildPerturbationLandscape_quick
- run_fgsea2
- s4_label_propagation.m
- s5_module_gene_anno.m
- sbe_laplacian_matrix
- scInTime
- sctenifoldknk
- sctenifoldnet
- sc_pcnetdenoised
- test_code.m
+ten/+xct
@SingleCellExperiment
- assigncelltype
- clustercells
- embedcells
- estimatecellcycle
- estimatepotency
- onestepraw2anno
- qcfilterwhitelist
- SingleCellExperiment
- sortcells
private
- Cal_NMI
- colorgradient
- countmember
- distcorr
- fLOESS
- gscatter3
- gscatter3b
- isnormalized
- i_myupdatefcn1
- i_myupdatefcn2
- i_myupdatefcn3
- i_myupdatefcnx
- i_myupdatefcnxy
- i_toolboxdependencyanalysis.m
- i_view5d
- jarpat.m
- jarpat_x
- lmsvd
- lowess.m
- mmread
- movzeros
- natsort
- ppval
- rsvd
- rsvd2
- sc_celltypebrushed
- sc_celltypeexplore.m
- sc_explorer2
- SNN_fun
- splinefit
- ws_distance
resources/HPA_Single_Cell_Type_Atlas
tensor_toolbox
tensor_toolbox/@ktensor
- arrange
- datadisp
- disp
- display
- double
- end
- extract
- fixsigns
- full
- innerprod
- isequal
- isscalar
- issymmetric
- ktensor.m
- mask
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- mtimes
- mttkrp
- ncomponents
- ndims
- norm
- normalize
- nvecs
- permute
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- score
- size
- subsasgn
- subsref
- symmetrize
- times
- tocell
- tovec
- ttm
- ttv
- uminus
- update
- uplus
- viz
tensor_toolbox/@tenmat
- ctranspose
- disp
- display
- double
- end
- minus
- mtimes
- norm
- plus
- size
- subsasgn
- subsref
- tenmat.m
- tsize
- uminus
- uplus
tensor_toolbox/@tensor
- and
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- contract
- disp
- display
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- eq
- exp
- find
- full
- ge
- gt
- innerprod
- isequal
- isscalar
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- ldivide
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- lt
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- mldivide
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- ndims
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- nvecs
- or
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- tenfun
- tensor.m
- times
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- ttv
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- xor
tensor_toolbox/@ttensor
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