Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / theislab/scCODA issues and pull requests

#102 - What is the reasonable FDR value? 0.05?

Issue - State: open - Opened by mainharryHR 4 months ago - 1 comment

#101 - Value Error when runing mod.CompositionalAnalysis

Issue - State: closed - Opened by boluofen 4 months ago - 7 comments

#100 - alr t test

Issue - State: open - Opened by feanaros 4 months ago - 3 comments

#99 - Intra-sample abundances

Issue - State: open - Opened by n-hal 5 months ago - 1 comment

#98 - How to plot the final result?

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

#97 - Multiple comparisons

Issue - State: closed - Opened by mainharryHR 6 months ago - 2 comments

#96 - Using continuous variables yield weird results.

Issue - State: closed - Opened by Marwansha 7 months ago - 3 comments

#95 - Bug in viz.boxplots function (and possibly others)

Issue - State: open - Opened by reemagit 9 months ago - 3 comments

#94 - How to compare multiple groups with sccoda

Issue - State: closed - Opened by karenlawwc 9 months ago - 7 comments

#93 - interpreting the output with the issue of compositionality.

Issue - State: closed - Opened by Marwansha 9 months ago - 6 comments

#92 - module 'pertpy.plot' has no attribute 'coda'

Issue - State: closed - Opened by Marwansha 9 months ago - 1 comment

#91 - Influence of number of cells in parameterization

Issue - State: closed - Opened by auesro 10 months ago - 6 comments

#90 - Usage without replicates ?

Issue - State: closed - Opened by divyanshusrivastava 10 months ago - 2 comments

#89 - Covariate has non-unique values

Issue - State: closed - Opened by schroeme 10 months ago - 2 comments

#88 - Use the model with multiple covariants including numeric ones?

Issue - State: closed - Opened by RunyuXia 11 months ago - 1 comment

#87 - mixed effect model

Issue - State: closed - Opened by t-a-m-i 12 months ago - 1 comment

#85 - Additive model with batch

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

#84 - Final Parameter and log2-fold change have different signs

Issue - State: closed - Opened by PauBadiaM over 1 year ago - 6 comments

#83 - Tutorial for R/reticulate

Issue - State: closed - Opened by ConDem94 over 1 year ago - 3 comments

#82 - model comparison using LOO/WAIC

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

#81 - additive effects and interaction terms

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

#80 - Exporting Summary Results

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

#79 - Error when num_burnins > num_results

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

#78 - AttributeError: module 'arviz' has no attribute 'data'

Issue - State: closed - Opened by jhong26 over 1 year ago - 2 comments

#77 - Questions about generalizability to other NGS datasets

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

#75 - conda compatibility

Issue - State: closed - Opened by Nusob888 almost 2 years ago - 4 comments

#74 - Bootstrap or splitting my samples

Issue - State: closed - Opened by dekan-aleksandr almost 2 years ago - 2 comments

#73 - Replace sklearn dependency with scikit-learn

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

#72 - scCODA p-values?

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

#71 - access sim_results.summary() for further analysis in R

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

#70 - Feature Request: Automatically print significance indicator in boxplots

Issue - State: open - Opened by alefrol638 almost 2 years ago - 1 comment

#69 - Feature Request: log10 scaling for Boxplots

Issue - State: closed - Opened by alefrol638 almost 2 years ago - 1 comment

#68 - All cell types as reference loop error

Issue - State: closed - Opened by AClab-sgarcia about 2 years ago - 17 comments

#67 - Understanding inclusion probability

Issue - State: closed - Opened by auesro about 2 years ago - 4 comments

#66 - Zero log2-fold change but credible change being identified?

Issue - State: closed - Opened by learning-MD about 2 years ago - 3 comments

#65 - loading data with dat.from_scanpy

Issue - State: closed - Opened by HosseinMousavi about 2 years ago - 2 comments

#64 - Cell identities displaying as numbers?

Issue - State: closed - Opened by potterae over 2 years ago - 1 comment

#62 - est_fdr did not change the result

Issue - State: closed - Opened by grimwoo over 2 years ago - 6 comments

#61 - P value (FDR) and interpretation of "Final Parameter"

Issue - State: closed - Opened by grimwoo over 2 years ago - 2 comments

#60 - Is the input data expected by scCODA the size of the cell type for each sample?

Issue - State: closed - Opened by altairwei over 2 years ago - 1 comment

#59 - Update 0.1.8

Pull Request - State: closed - Opened by johannesostner over 2 years ago - 1 comment

#58 - Which tensorflow version to use?

Issue - State: closed - Opened by c-westhoven over 2 years ago - 3 comments

#57 - Influence of subtypes present in the dataset

Issue - State: closed - Opened by auesro over 2 years ago - 4 comments

#55 - col_wrap in utils.visualization.boxplots

Issue - State: closed - Opened by c-westhoven over 2 years ago - 1 comment

#54 - Importance of warnings/errors in model_scelltype_Time.sample_hmc() output

Issue - State: closed - Opened by Lopiniatre over 2 years ago - 1 comment

#53 - Looping over cell types to use as reference: discrepancy?

Issue - State: open - Opened by koenvandenberge over 2 years ago - 11 comments

#52 - verbose option for `sample_hmc`

Issue - State: closed - Opened by koenvandenberge over 2 years ago - 1 comment

#51 - How to save the results as dataframe or show the whole summary?

Issue - State: closed - Opened by Zifeng-L over 2 years ago - 2 comments

#50 - Stacked barplot not working

Issue - State: closed - Opened by learning-MD over 2 years ago - 2 comments

#49 - Allow set random seed for reproducibility in `CompositionalAnalysis` objects

Pull Request - State: open - Opened by yihming over 2 years ago - 1 comment

#48 - sample_hmc() fails without error when NAs are present

Issue - State: closed - Opened by RoganGrant almost 3 years ago - 1 comment

#47 - Obtain p-values for cell type abundance effect

Issue - State: closed - Opened by mxposed almost 3 years ago - 1 comment

#46 - Exit code 134

Issue - State: closed - Opened by RachellyN almost 3 years ago - 6 comments

#45 - Zero Fold-change in scCODA results

Issue - State: closed - Opened by RachellyN almost 3 years ago - 3 comments

#43 - Include Haber data in package

Pull Request - State: closed - Opened by mbuttner almost 3 years ago - 1 comment

#42 - Fix docs

Issue - State: closed - Opened by dawe about 3 years ago - 2 comments

#41 - Mismatched sample labels

Issue - State: closed - Opened by mhulke about 3 years ago - 8 comments

#40 - WARNING:tensorflow:@custom_gradient grad_fn has 'variables' in signature

Issue - State: closed - Opened by Elhl93 about 3 years ago - 5 comments

#39 - Cannot import sccoda.util.comp_ana

Issue - State: closed - Opened by neurOnur about 3 years ago - 4 comments

#38 - MCMC reproducibility

Issue - State: closed - Opened by orrzor about 3 years ago - 2 comments

#37 - Result reproducibility issues depending on Python version

Issue - State: closed - Opened by Christophe29-BZH over 3 years ago - 3 comments

#36 - Error in version update_0.1.3: 'Inclusion probability'

Issue - State: closed - Opened by jdhenaos over 3 years ago - 1 comment

#35 - Including Bad Cells in Model

Issue - State: closed - Opened by kanefos over 3 years ago - 2 comments

#34 - how to assess sccoda results

Issue - State: closed - Opened by FADHLyemen over 3 years ago - 3 comments

#33 - Optimal tuning of parameters for estimation

Issue - State: closed - Opened by fbrundu over 3 years ago - 3 comments

#32 - add_dots parameter not respecting hue_order arg in boxplot

Issue - State: closed - Opened by fbrundu over 3 years ago - 4 comments

#31 - How to approach inference on data with multiple timepoints

Issue - State: closed - Opened by fbrundu over 3 years ago - 2 comments

#30 - Beta binomial and ANCOMBC

Pull Request - State: closed - Opened by mbuttner over 3 years ago

#29 - which condition scCODA can work with?

Issue - State: closed - Opened by FADHLyemen over 3 years ago - 7 comments

#28 - Bump tensorflow from 2.3.2 to 2.5.0

Pull Request - State: closed - Opened by dependabot[bot] over 3 years ago - 1 comment
Labels: dependencies

#27 - how to select cell reference

Issue - State: closed - Opened by FADHLyemen over 3 years ago - 5 comments

#26 - Test All Pairwise Comparisons

Issue - State: closed - Opened by kanefos over 3 years ago - 4 comments

#25 - Solved: ImportError: cannot import name 'CloudPickler'

Issue - State: closed - Opened by kanefos over 3 years ago

#24 - how to make one condition as a reference

Issue - State: closed - Opened by FADHLyemen over 3 years ago - 2 comments

#23 - "division by zero" error

Issue - State: closed - Opened by miligeo18 over 3 years ago - 7 comments

#22 - Add scikit-bio as dependecies

Issue - State: closed - Opened by b-schubert over 3 years ago - 1 comment

#21 - Release 0.1.2

Pull Request - State: closed - Opened by johannesostner over 3 years ago - 1 comment

#20 - Segmentation Fault

Issue - State: closed - Opened by smorabit almost 4 years ago - 1 comment

#19 - Added 'level_order' for custom ordering in stacked_barplot

Pull Request - State: closed - Opened by redst4r almost 4 years ago - 1 comment

#18 - Bump tensorflow from 2.3.0 to 2.4.0

Pull Request - State: closed - Opened by dependabot[bot] almost 4 years ago - 2 comments
Labels: dependencies

#17 - Release 0.1

Pull Request - State: closed - Opened by johannesostner almost 4 years ago - 1 comment

#16 - different results in different runs

Issue - State: closed - Opened by bsierieb1 almost 4 years ago - 8 comments

#15 - sample_hmc error

Issue - State: closed - Opened by bsierieb1 almost 4 years ago - 6 comments

#14 - import from scanpy

Issue - State: closed - Opened by bsierieb1 almost 4 years ago - 7 comments

#13 - Warning triggered tf.function retracing

Issue - State: closed - Opened by b-schubert about 4 years ago - 1 comment

#12 - reimplemented no baselline model; added model for time-based effects

Pull Request - State: closed - Opened by johannesostner about 4 years ago

#11 - Merge dev into master for ML Hackathon

Pull Request - State: closed - Opened by johannesostner about 4 years ago - 1 comment

#10 - added functions for data visualization, extended model comparison

Pull Request - State: closed - Opened by johannesostner about 4 years ago - 1 comment

#9 - How to save `sim_results` object?

Issue - State: closed - Opened by mbuttner over 4 years ago - 3 comments

#8 - Error in samle_hmc()

Issue - State: closed - Opened by le-ander over 4 years ago - 3 comments

#7 - boostrapping on posterior samples for inclusion prob variance

Issue - State: closed - Opened by b-schubert over 4 years ago
Labels: enhancement

#6 - API design comment

Issue - State: closed - Opened by giovp over 4 years ago - 2 comments

#5 - Error + question on model usage

Issue - State: closed - Opened by giovp over 4 years ago - 2 comments

#4 - logfoldchange always -0.430725 for non significant classes

Issue - State: closed - Opened by le-ander over 4 years ago - 2 comments