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const-ae

13 indexed repositories · View on GitHub

ggsignif
Easily add significance brackets to your ggplots

R · 614 stars
ggupset
Combination matrix axis for 'ggplot2' to create 'UpSet' plots

R · 399 stars
glmGamPoi
Fit Gamma-Poisson Generalized Linear Models Reliably

R · 126 stars
tidygenomics
Tidy Verbs for Dealing with Genomic Data Frames https://const-ae.github.io/tidygenomics/

R · 106 stars
lemur
Latent Embedding Multivariate Regression

R · 102 stars
linear_perturbation_prediction-Paper

HTML · 95 stars
sparseMatrixStats
Implementation of the matrixStats API for sparse matrices

R · 55 stars
transformGamPoi-Paper

HTML · 29 stars
proDA
Protein Differential Abundance for Label-Free Mass Spectrometry https://const-ae.github.io/proDA/

R · 24 stars
transformGamPoi
Variance stabilizing transformation for Gamma Poisson distributed data

R · 22 stars
Neural_Network_DNA_Demo
Jupyter Notebook to demonstrate the use of Neural Networks for Transcription Factor Binding Site Prediction

Jupyter Notebook · 13 stars
CoronaDensity

HTML · 3 stars
polarstation
Tidy helper functions for polars that can peek at the full data.

Python · 1 star

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geom_signif - all comparisons dissappear when one comparison has missings Open

const-ae/ggsignif#126 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Significance stars are misaligned when using "NS" as well Open

const-ae/ggsignif#127 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
ggsignif results don't match with anova significance Open

reprex

const-ae/ggsignif#128 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Use cross symbol when p <.10? Open

const-ae/ggsignif#129 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
How do I hide the no significant (NS) comparisons? Open

const-ae/ggsignif#131 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Adding significance bar on coupled boxplots Open

const-ae/ggsignif#132 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Show exact p value in comparisons Open

enhancement

const-ae/ggsignif#137 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
ggsignif facetting issue - Missing significance labels in certain facets Open

const-ae/ggsignif#138 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Label missing if identical Open

const-ae/ggsignif#140 · 4 comments · 1 reaction · 0 assignees · Indexed Sep 15, 2026
ggcompare：Implement layer-level P value correction. Open

const-ae/ggsignif#143 · 6 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Question Open

const-ae/ggsignif#145 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
P-value from Dunn's test Open

const-ae/ggsignif#146 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
how to set tip_length and y_position ? Open

const-ae/ggsignif#150 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Calculating Significance between legend variables in different groups Open

const-ae/ggsignif#151 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
import_MaxQuant filter Open

const-ae/proDA#6 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Why Intensity over iBAQ? Open

const-ae/proDA#11 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
dist_approx() not stable Open

const-ae/proDA#13 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
different results for some proteins depending test used. Open

const-ae/proDA#14 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Equivalent of Fold-Change analysis? Open

const-ae/proDA#16 · 8 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Pre-filtering steps and requirements per sample Open

const-ae/proDA#17 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
NA dropout_curve parameters Open

const-ae/proDA#19 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
constitutively missing peptides/proteins across "runs" Open

const-ae/proDA#20 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Error in nlminb(), NA/NaN gradient evaluation Open

const-ae/proDA#23 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Convergence Issues Open

const-ae/proDA#24 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Error in `if (sign(objective_fun(min_var)) == sign(objective_fun(max_var)))` A bool needed Open

const-ae/proDA#25 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Tests fail on i386 (really i686): ailure: qres.gampoi can handle other weird values (@test-residuals.R#112) `a` is not strictly more than `b`. Difference: 0 Open

const-ae/glmGamPoi#15 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Use for pseudobulk differential expression - advantages & logFC values Open

const-ae/glmGamPoi#22 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
pseudobulk_by apparently dropping columns Open

const-ae/glmGamPoi#23 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
determining the less trustworthy log2fc values Open

const-ae/glmGamPoi#27 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
test_de failing with on_disk models Open

const-ae/glmGamPoi#33 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Too many DEGs? Open

const-ae/glmGamPoi#35 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Core Usage Open

const-ae/glmGamPoi#36 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Can't install the package on MacOS Monterey Open

const-ae/glmGamPoi#37 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Error in pseudobulk step Open

const-ae/glmGamPoi#39 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
compare multiple pairs concurrently Open

const-ae/glmGamPoi#40 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
glmGamPoi scales cubically with the number of design matrix columns Open

const-ae/glmGamPoi#41 · 5 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Error in handle_design_parameter(design, data, col_data, reference_level) : Too few replicates / too many coefficients to fit model. Open

const-ae/glmGamPoi#42 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Compatibility with R 3 Open

const-ae/glmGamPoi#48 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
compilation error Open

const-ae/glmGamPoi#49 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Standard error of the overdispersion estimates Open

const-ae/glmGamPoi#50 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
HDF5Array is not available for package glmGamPoi Open

const-ae/glmGamPoi#54 · 4 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
[FR] Implement `logLik.glmGamPoi` Open

const-ae/glmGamPoi#58 · 2 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
NaNs in standard errors of LFC Open

const-ae/glmGamPoi#69 · 1 comment · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Question regarding the difference of running glmGamPoi on a subset of data or on the whole data. Open

const-ae/glmGamPoi#72 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Potential discrepancy in second derivative of log-likelihood (Hessian) for overdispersion parameter \theta in overdispersion.cpp Open

const-ae/glmGamPoi#74 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Question regarding the role of xim in overdispersion theta estimation Open

const-ae/glmGamPoi#75 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
Why do not return shrunken dispersion as the ultimate overdispersion? Open

const-ae/glmGamPoi#76 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
chop output differs between eager and lazy mode Open

const-ae/polarstation#5 · 0 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
installation error Open

const-ae/lemur#1 · 3 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026
>2 conditions Open

const-ae/lemur#4 · 9 comments · 0 reactions · 0 assignees · Indexed Sep 15, 2026

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