Ecosyste.ms: Issues

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GitHub / quadbio/Pando issues and pull requests

#64 - model overfitting

Issue - State: open - Opened by tkisss 5 months ago

#64 - model overfitting

Issue - State: open - Opened by tkisss 5 months ago

#63 - Pando output - enhancer regions

Issue - State: open - Opened by valentinaOpazo 5 months ago

#63 - Pando output - enhancer regions

Issue - State: open - Opened by valentinaOpazo 5 months ago

#62 - regions parameter in initate_grn()

Issue - State: open - Opened by sylestiel 6 months ago - 4 comments

#62 - regions parameter in initate_grn()

Issue - State: open - Opened by sylestiel 6 months ago - 4 comments

#61 - Question: where to find tutorial seurat object dataset

Issue - State: closed - Opened by jennymoon90 6 months ago - 1 comment

#61 - Question: where to find tutorial seurat object dataset

Issue - State: closed - Opened by jennymoon90 6 months ago - 1 comment

#60 - a subgraph of the GRN specifying only one "target gene"

Issue - State: closed - Opened by m03077yhtnt 7 months ago - 1 comment

#60 - a subgraph of the GRN specifying only one "target gene"

Issue - State: closed - Opened by m03077yhtnt 7 months ago - 1 comment

#56 - plot_network_graph() only plot target genes

Issue - State: open - Opened by zhenzuo2 8 months ago - 1 comment

#56 - plot_network_graph() only plot target genes

Issue - State: open - Opened by zhenzuo2 8 months ago - 1 comment

#55 - Questions on integration and interpretation

Issue - State: closed - Opened by JABioinf 8 months ago - 3 comments

#55 - Questions on integration and interpretation

Issue - State: closed - Opened by JABioinf 8 months ago - 3 comments

#53 - Error in find_motifs with invalid version slot in SeuratPlus object

Issue - State: open - Opened by jsacco1 9 months ago - 5 comments

#53 - Error in find_motifs with invalid version slot in SeuratPlus object

Issue - State: open - Opened by jsacco1 9 months ago - 5 comments

#52 - Advice about a dataset with conditions

Issue - State: open - Opened by AmelZulji 10 months ago - 4 comments

#52 - Advice about a dataset with conditions

Issue - State: open - Opened by AmelZulji 10 months ago - 4 comments

#50 - infer_grn errors

Issue - State: open - Opened by bjstewart1 11 months ago

#50 - infer_grn errors

Issue - State: open - Opened by bjstewart1 11 months ago

#49 - Question: celltype-specific GRN

Issue - State: closed - Opened by tkisss 11 months ago - 2 comments

#49 - Question: celltype-specific GRN

Issue - State: closed - Opened by tkisss 11 months ago - 2 comments

#48 - input data normalisation

Issue - State: open - Opened by bjstewart1 11 months ago - 7 comments

#48 - input data normalisation

Issue - State: open - Opened by bjstewart1 11 months ago - 7 comments

#47 - Where is the Sample Data from Vignettes?

Issue - State: closed - Opened by TeodoraTockovska 12 months ago - 1 comment

#46 - `coef()` results was changed

Issue - State: closed - Opened by mkojima123 about 1 year ago - 2 comments

#46 - `coef()` results was changed

Issue - State: closed - Opened by mkojima123 about 1 year ago - 2 comments

#45 - where to download the tutorial data

Issue - State: closed - Opened by GouQiao about 1 year ago

#44 - error in initiate_grn()

Issue - State: closed - Opened by GouQiao about 1 year ago - 2 comments

#44 - error in initiate_grn()

Issue - State: closed - Opened by GouQiao about 1 year ago - 2 comments

#43 - Run pando on dataset with different conditions

Issue - State: closed - Opened by JoreVW about 1 year ago - 1 comment

#43 - Run pando on dataset with different conditions

Issue - State: closed - Opened by JoreVW about 1 year ago - 1 comment

#42 - Error:infer_grn(),

Issue - State: open - Opened by wxpbioinfo over 1 year ago - 4 comments

#42 - Error:infer_grn(),

Issue - State: open - Opened by wxpbioinfo over 1 year ago - 4 comments

#41 - Update website link in the readme

Pull Request - State: closed - Opened by Marius1311 over 1 year ago

#41 - Update website link in the readme

Pull Request - State: closed - Opened by Marius1311 over 1 year ago

#40 - initiate_grn error

Issue - State: closed - Opened by zhijunyuu over 1 year ago - 3 comments

#40 - initiate_grn error

Issue - State: closed - Opened by zhijunyuu over 1 year ago - 3 comments

#39 - running time of Pando

Issue - State: closed - Opened by crystal0721 over 1 year ago - 1 comment

#39 - running time of Pando

Issue - State: closed - Opened by crystal0721 over 1 year ago - 1 comment

#38 - scRNA data only

Issue - State: closed - Opened by dimurali93 over 1 year ago - 1 comment

#38 - scRNA data only

Issue - State: closed - Opened by dimurali93 over 1 year ago - 1 comment

#37 - infer_grn() parallelization cores not delivering results

Issue - State: closed - Opened by stran94 over 1 year ago - 1 comment

#37 - infer_grn() parallelization cores not delivering results

Issue - State: closed - Opened by stran94 over 1 year ago - 1 comment

#36 - ERROR in GRN inference

Issue - State: open - Opened by Usamahussein551980 over 1 year ago - 2 comments

#36 - ERROR in GRN inference

Issue - State: open - Opened by Usamahussein551980 over 1 year ago - 2 comments

#35 - Question: Can Pando be used on an unpaired multiomic dataset?

Issue - State: closed - Opened by mitchTwoTimes over 1 year ago - 1 comment

#34 - I need your help

Issue - State: closed - Opened by Usamahussein551980 over 1 year ago - 3 comments

#33 - Question: feature selection for network plots, UMAP embedding

Issue - State: closed - Opened by kstrotjohann over 1 year ago - 1 comment

#33 - Question: feature selection for network plots, UMAP embedding

Issue - State: closed - Opened by kstrotjohann over 1 year ago - 1 comment

#32 - Error in as.igraph.vs(graph, from) : Invalid vertex names

Issue - State: open - Opened by mitchTwoTimes over 1 year ago - 2 comments

#32 - Error in as.igraph.vs(graph, from) : Invalid vertex names

Issue - State: open - Opened by mitchTwoTimes over 1 year ago - 2 comments

#31 - Question: How to customize GRN plot with metadata

Issue - State: closed - Opened by mitchTwoTimes over 1 year ago - 1 comment

#29 - Error in infer_grn()

Issue - State: open - Opened by TerezaClarence over 1 year ago - 5 comments

#29 - Error in infer_grn()

Issue - State: open - Opened by TerezaClarence over 1 year ago - 5 comments

#28 - Direction of regulation / highlighting TFs in the network plot

Issue - State: closed - Opened by kstrotjohann over 1 year ago - 2 comments

#28 - Direction of regulation / highlighting TFs in the network plot

Issue - State: closed - Opened by kstrotjohann over 1 year ago - 2 comments

#27 - phastCons for Mus musculus

Issue - State: closed - Opened by sylestiel over 1 year ago - 3 comments

#27 - phastCons for Mus musculus

Issue - State: closed - Opened by sylestiel over 1 year ago - 3 comments

#26 - Infer_grn Function Returning Error

Issue - State: closed - Opened by Sandman-1 over 1 year ago - 21 comments

#26 - Infer_grn Function Returning Error

Issue - State: closed - Opened by Sandman-1 over 1 year ago - 21 comments

#25 - Update grn.R

Pull Request - State: open - Opened by Sandman-1 over 1 year ago

#25 - Update grn.R

Pull Request - State: open - Opened by Sandman-1 over 1 year ago

#24 - Update grn.R

Pull Request - State: open - Opened by Sandman-1 over 1 year ago - 1 comment

#24 - Update grn.R

Pull Request - State: open - Opened by Sandman-1 over 1 year ago - 1 comment

#23 - Error with plot_tf_network

Issue - State: closed - Opened by Ping-lin14 almost 2 years ago - 1 comment

#23 - Error with plot_tf_network

Issue - State: closed - Opened by Ping-lin14 almost 2 years ago - 1 comment

#22 - normalization

Issue - State: closed - Opened by xujiahao778899 almost 2 years ago

#22 - normalization

Issue - State: closed - Opened by xujiahao778899 almost 2 years ago

#21 - Question on custom motif sets

Issue - State: closed - Opened by DanielYuhangLi almost 2 years ago - 2 comments
Labels: question

#21 - Question on custom motif sets

Issue - State: closed - Opened by DanielYuhangLi almost 2 years ago - 2 comments
Labels: question

#20 - The model for repressor

Issue - State: closed - Opened by yamajackr almost 2 years ago - 1 comment
Labels: enhancement, question

#20 - The model for repressor

Issue - State: closed - Opened by yamajackr almost 2 years ago - 1 comment
Labels: enhancement, question

#19 - Module activity between branches (and over pseudotime)

Issue - State: closed - Opened by anderswe almost 2 years ago - 6 comments
Labels: question

#19 - Module activity between branches (and over pseudotime)

Issue - State: closed - Opened by anderswe almost 2 years ago - 6 comments
Labels: question

#18 - Error "attempt to select less than one element in integerOneIndex"

Issue - State: closed - Opened by lingfeiwang almost 2 years ago - 13 comments

#18 - Error "attempt to select less than one element in integerOneIndex"

Issue - State: closed - Opened by lingfeiwang almost 2 years ago - 13 comments

#17 - "not-yet-implemented 'Matrix[<-' method"

Issue - State: closed - Opened by DanielYuhangLi almost 2 years ago - 3 comments
Labels: bug

#17 - "not-yet-implemented 'Matrix[<-' method"

Issue - State: closed - Opened by DanielYuhangLi almost 2 years ago - 3 comments
Labels: bug

#16 - Installation failure due to Matrix.utils dependency

Issue - State: closed - Opened by vkartha almost 2 years ago - 4 comments
Labels: bug

#16 - Installation failure due to Matrix.utils dependency

Issue - State: closed - Opened by vkartha almost 2 years ago - 4 comments
Labels: bug

#15 - Test data/ vignette data accessibility

Issue - State: closed - Opened by dimurali93 almost 2 years ago - 1 comment
Labels: documentation, question

#15 - Test data/ vignette data accessibility

Issue - State: closed - Opened by dimurali93 almost 2 years ago - 1 comment
Labels: documentation, question

#14 - badge fix

Pull Request - State: closed - Opened by FrickTobias almost 2 years ago - 1 comment

#14 - badge fix

Pull Request - State: closed - Opened by FrickTobias almost 2 years ago - 1 comment

#13 - badge fix

Pull Request - State: closed - Opened by FrickTobias almost 2 years ago

#13 - badge fix

Pull Request - State: closed - Opened by FrickTobias almost 2 years ago

#12 - plot_module_metrics(muo_data)

Issue - State: closed - Opened by zhenzuo2 almost 2 years ago - 1 comment
Labels: bug