saezlab/liana-py issues and pull requests

#68 - Scseqcomm dev

Pull Request - State: closed - Opened by BaldanMatt over 1 year ago - 3 comments

#67 - li.multi.df_to_lr function gave gene Value error

Issue - State: closed - Opened by Hweeseon over 1 year ago - 4 comments
Labels: bug, help wanted

#66 - Help understanding causal network output

Issue - State: closed - Opened by ebasto over 1 year ago - 1 comment
Labels: help wanted

#65 - 1.0.2

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

#64 - AttributeError: module 'corneto.methods.carnival' has no attribute 'select_mip_solver'

Issue - State: closed - Opened by FADHLyemen over 1 year ago - 11 comments
Labels: bug, help wanted

#63 - 1.0.0

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

#62 - Release 1.0.0

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

#61 - Add product as local score

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

#60 - Cellphone DB (and other database versions)

Issue - State: open - Opened by SimonDMurray over 1 year ago - 5 comments
Labels: enhancement

#59 - AttributeError: module 'liana.method' has no attribute 'build_prior_network'

Issue - State: closed - Opened by qijt123 over 1 year ago - 4 comments
Labels: bug, help wanted

#58 - Merge 1.0.0a2

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

#57 - By default do not convert views to `csr_matrix` when building `MistyData`.

Issue - State: closed - Opened by PauBadiaM over 1 year ago - 1 comment
Labels: enhancement

#56 - Add aggregate function for MISTy models (extend plots)

Issue - State: open - Opened by PauBadiaM over 1 year ago - 3 comments
Labels: enhancement

#55 - Sort interactions names in `li.pl.tileplot` by the `orderby` argument

Issue - State: closed - Opened by PauBadiaM over 1 year ago - 2 comments
Labels: enhancement

#54 - Clarification regarding hypothesis testing

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

#54 - Clarification regarding hypothesis testing

Issue - State: open - Opened by inofechm over 1 year ago - 1 comment

#53 - Missing Resources

Issue - State: closed - Opened by pallikheni over 1 year ago - 3 comments
Labels: bug, help wanted

#53 - Missing Resources

Issue - State: open - Opened by pallikheni over 1 year ago - 1 comment
Labels: bug, help wanted

#52 - What was steady_rank and why is it removed?

Issue - State: open - Opened by dnjst over 1 year ago - 1 comment

#52 - What was steady_rank and why is it removed?

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

#51 - KeyError: missing elements

Issue - State: open - Opened by rr-Yiran over 1 year ago - 3 comments
Labels: bug, help wanted

#51 - KeyError: missing elements

Issue - State: closed - Opened by rr-Yiran over 1 year ago - 4 comments
Labels: bug, help wanted

#50 - Dev

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

#50 - Dev

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

#49 - Bug report for a tileplot function.

Issue - State: closed - Opened by partrita over 1 year ago - 1 comment
Labels: enhancement

#49 - Bug report for a tileplot function.

Issue - State: closed - Opened by partrita over 1 year ago - 1 comment
Labels: enhancement

#48 - create metalinks estimation function

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

#48 - create metalinks estimation function

Pull Request - State: closed - Opened by EliasFarr over 1 year ago - 2 comments

#47 - Dev

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

#47 - Dev

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

#46 - Clean up MISTy's pipeline

Issue - State: closed - Opened by dbdimitrov over 1 year ago
Labels: enhancement

#46 - Clean up MISTy's pipeline

Issue - State: open - Opened by dbdimitrov over 1 year ago
Labels: enhancement

#45 - Metabolite-mediated CCC tutorial

Issue - State: closed - Opened by dbdimitrov over 1 year ago
Labels: enhancement

#45 - Metabolite-mediated CCC tutorial

Issue - State: open - Opened by dbdimitrov over 1 year ago
Labels: enhancement

#44 - Split global from local scores

Issue - State: closed - Opened by dbdimitrov over 1 year ago
Labels: enhancement

#44 - Split global from local scores

Issue - State: open - Opened by dbdimitrov over 1 year ago
Labels: enhancement

#43 - Verbosity/Logging

Issue - State: open - Opened by dbdimitrov over 1 year ago
Labels: enhancement

#43 - Verbosity/Logging

Issue - State: closed - Opened by dbdimitrov over 1 year ago
Labels: enhancement

#42 - keep psbulk stats when converting to MuData

Pull Request - State: closed - Opened by demian1 over 1 year ago

#42 - keep psbulk stats when converting to MuData

Pull Request - State: open - Opened by demian1 over 1 year ago

#41 - Single-cell Multi-omics tutorial

Issue - State: closed - Opened by dbdimitrov over 1 year ago
Labels: enhancement

#41 - Multi-omics tutorials

Issue - State: open - Opened by dbdimitrov over 1 year ago
Labels: enhancement

#40 - Set scanpy as a "common" dependency

Issue - State: open - Opened by dbdimitrov over 1 year ago

#40 - Set scanpy as a "common" dependency

Issue - State: open - Opened by dbdimitrov over 1 year ago

#39 - LIANA+ merge

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

#39 - LIANA+ merge

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

#38 - Move functions from liana to corneto

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

#38 - Move functions from liana to corneto

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

#37 - Improve corneto integration, update notebook and refactor

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

#37 - Improve corneto integration, update notebook and refactor

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

#36 - Improve corneto integration

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

#35 - About 'expr_prop' in rank aggregates

Issue - State: closed - Opened by nrclaudio over 1 year ago - 4 comments

#35 - About 'expr_prop' in rank aggregates

Issue - State: closed - Opened by nrclaudio over 1 year ago - 4 comments

#34 - Getting TypeError: Accessing a group is done with bytes or str, not <class 'tuple'> when running `mu.tl.mofa()`

Issue - State: closed - Opened by thjimmylee over 1 year ago - 3 comments
Labels: bug, help wanted

#33 - added preprocessing needed for CORNETO

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

#33 - added preprocessing needed for CORNETO

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

#32 - MuData & Decoupler-py as dependencies

Issue - State: closed - Opened by dbdimitrov over 1 year ago
Labels: bug

#32 - MuData & Decoupler-py as dependencies

Issue - State: closed - Opened by dbdimitrov over 1 year ago
Labels: bug

#31 - Add support for causal network search with corneto

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

#31 - Add support for causal network search with corneto

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

#30 - Support for network optimization through corneto

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

#30 - Support for network optimization through corneto

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

#29 - added remove_hvg_marker_genes function

Pull Request - State: closed - Opened by demian1 over 1 year ago

#29 - added remove_hvg_marker_genes function

Pull Request - State: open - Opened by demian1 over 1 year ago

#28 - Check sample_key & groupby

Issue - State: closed - Opened by dbdimitrov over 1 year ago - 1 comment
Labels: enhancement

#28 - Check sample_key & groupby

Issue - State: open - Opened by dbdimitrov over 1 year ago
Labels: enhancement

#27 - Improve documentation

Issue - State: closed - Opened by dbdimitrov over 1 year ago
Labels: enhancement

#26 - fixed bug in get_factor_loadings

Pull Request - State: closed - Opened by demian1 almost 2 years ago - 1 comment

#25 - Remove usage of deprecated np.float

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

#24 - Numpy 1.24.x compatibility

Issue - State: closed - Opened by DriesSchaumont almost 2 years ago - 2 comments
Labels: bug, help wanted

#23 - Run permutation-based methods with `n_perms=0`

Issue - State: closed - Opened by PauBadiaM almost 2 years ago - 2 comments
Labels: enhancement

#22 - Automatic sorting of LR results

Issue - State: closed - Opened by PauBadiaM almost 2 years ago - 2 comments
Labels: enhancement

#21 - limit plotting in li.pl.dotplot to selected ligands/receptors

Issue - State: closed - Opened by JuHey almost 2 years ago - 4 comments
Labels: enhancement, help wanted

#20 - Metalinks merge

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

#19 - added slim version of misty

Pull Request - State: closed - Opened by schae211 almost 2 years ago

#18 - v0.1.9

Pull Request - State: closed - Opened by dbdimitrov almost 2 years ago - 4 comments

#17 - decoupler feature filtering

Pull Request - State: closed - Opened by demian1 almost 2 years ago - 2 comments

#16 - make merge on index compatbile with pd in 3.7

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

#15 - fix issue with missing index name

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

#14 - Feature supp add

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

#13 - Only use adata.uns['liana_res'] if inplace==False

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

#12 - SyntaxError in Python 3.7

Issue - State: closed - Opened by pluto-the-lost about 2 years ago - 2 comments
Labels: bug, help wanted

#11 - Hypothesis-testing for comparisons between conditions

Issue - State: closed - Opened by grst about 2 years ago - 8 comments
Labels: enhancement

#10 - Error with import liana

Issue - State: closed - Opened by inofechm about 2 years ago - 5 comments
Labels: bug, help wanted

#9 - Querying Pypath & BioCypher knowledge graph

Issue - State: open - Opened by dbdimitrov about 2 years ago - 1 comment
Labels: enhancement

#8 - Added option to pass parameters directly to tensor-cell2cell

Pull Request - State: closed - Opened by earmingol about 2 years ago - 1 comment

#7 - Option to pass tensor_c2c parameters from liana

Issue - State: closed - Opened by earmingol about 2 years ago - 1 comment
Labels: enhancement

#6 - Visualize interactions across samples

Issue - State: closed - Opened by dbdimitrov about 2 years ago
Labels: enhancement

#5 - comparison across conditions

Issue - State: closed - Opened by Wulin-Tan about 2 years ago - 5 comments
Labels: enhancement

#4 - liana-py on other species

Issue - State: closed - Opened by Wulin-Tan about 2 years ago - 3 comments
Labels: enhancement

#3 - Generate Documentation /w Basic tutorial

Issue - State: closed - Opened by dbdimitrov over 2 years ago
Labels: documentation

#2 - Implement Geometric mean /w Perms

Issue - State: closed - Opened by dbdimitrov over 2 years ago
Labels: enhancement

#1 - Implement CellChat

Issue - State: closed - Opened by dbdimitrov over 2 years ago
Labels: enhancement

GitHub / saezlab/liana-py issues and pull requests