saezlab/progeny issues and pull requests

#61 - How to compare between groups?

Issue - State: open - Opened by XjtuZhangKun-lab about 1 month ago

#60 - Gene symbols used by PROGENY

Issue - State: closed - Opened by taraurselmann about 2 months ago - 2 comments

#59 - Layer counts isn't present in the assay object; returning NULL

Issue - State: closed - Opened by Noralii 2 months ago - 1 comment

#58 - Leaving out androgen pathway in tutorial?

Issue - State: closed - Opened by CB-postech 4 months ago - 1 comment

#57 - Prepare for upcoming Seurat v5 release

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

#56 - scatter plot adjustment

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

#55 - p-value for progeny on scRNA-seq clusters

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

#54 - Does the proteomics data can also use this tool to get the prediction of the pathway activity?

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

#53 - Which seurat assay to use for progeny

Issue - State: closed - Opened by cf98 over 1 year ago - 3 comments

#52 - p53 pathway target MDM2 weighting

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

#51 - Web page deployment faulty?

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

#50 - select new pathways

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

#49 - pkgdown site: removed old and added new assets

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

#48 - Update pkgdown site to bootstrap 5

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

#47 - Question of the Estrogen Pathway

Issue - State: closed - Opened by Caary about 2 years ago

#46 - Whether progeny could be used on gene-chip data

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

#45 - Return Gene List from progenyScatter

Issue - State: closed - Opened by HocheolJang426 over 2 years ago - 1 comment

#44 - Updated docs

Pull Request - State: closed - Opened by PauBadiaM over 2 years ago

#43 - Fixed plots on documentation

Pull Request - State: closed - Opened by PauBadiaM over 2 years ago

#42 - Modified documentation

Pull Request - State: closed - Opened by PauBadiaM over 2 years ago

#41 - NES for each pathway

Issue - State: closed - Opened by HocheolJang426 over 2 years ago - 1 comment

#40 - how to apply progeny on differential expression analysis result?

Issue - State: closed - Opened by shengqh almost 3 years ago - 2 comments

#39 - modified bulk vignette to use decoupleR

Pull Request - State: closed - Opened by adugourd almost 3 years ago

#38 - input data problem

Issue - State: closed - Opened by Tommaso12 about 3 years ago - 3 comments

#37 - object "model_human_full" is not exported by 'namespace:progeny''

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

#36 - Add new pathways

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

#35 - Cholmod error 'problem too large' at file ../Core/cholmod_dense.c,

Issue - State: closed - Opened by xyn0813 over 3 years ago - 1 comment

#34 - Exporting scatter plot to see full list of genes associated with pathways

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

#33 - Bias in 14 pathway collection

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

#32 - prepending progeny:: to the datasets in the getModel() call

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

#31 - Issue when Importing progeny for another package

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

#30 - Input Data Requirements Not Specified by Vignette

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

#29 - gene weights and directions

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

#28 - Possible to make corpus available?

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

#27 - progenyPerm - example is for progeny, not progenyPerm

Issue - State: closed - Opened by AGordonRobertson almost 4 years ago - 6 comments
Labels: enhancement

#26 - Error in t(expr[common_genes, , drop = FALSE]) %*% model[common_genes, : requires numeric/complex matrix/vector arguments

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

#25 - fix model data access

Pull Request - State: closed - Opened by jan-glx about 4 years ago - 3 comments

#24 - Incapability of handling large matrices.

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

#23 - Use of data slot instead of scale.data slot in Progeny.

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

#22 - Modify main progeny function to also search for human and mouse models in the local environment.

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

#21 - Progeny Function does control Gene Names duplicated

Issue - State: closed - Opened by alberto-valdeolivas about 4 years ago

#20 - progeny pathway score result differences with number of samples!

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

#19 - Buggy row names after permutation approach

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

#18 - only 11 pathways

Issue - State: closed - Opened by michelegentili93 over 4 years ago - 1 comment

#17 - Shift coordinates on the right plot in progenyScatter()

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

#16 - Expand progeny function to class data.frame -> progeny.data.frame()

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

#15 - Added ga

Pull Request - State: closed - Opened by christianholland over 4 years ago - 3 comments

#14 - Bioconductor update

Pull Request - State: closed - Opened by alberto-valdeolivas over 4 years ago

#13 - Error in t(expr[common_genes, , drop = FALSE]) %*% model[common_genes, : requires numeric/complex matrix/vector arguments

Issue - State: closed - Opened by yesitsjess over 4 years ago - 5 comments

#12 - How to use ConservedFootprints model with PROGENy wrapper

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

#11 - Missing Androgen, Estrogen and WNT?

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

#10 - WNT pathway

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

#9 - use with single gene list and scores

Issue - State: closed - Opened by blinggi almost 5 years ago - 2 comments

#8 - SPIA-modified z-scores to add information about position of gene in pathway

Issue - State: closed - Opened by jadeshi almost 6 years ago - 1 comment

#7 - RNA-seq: normalization, gene lengths

Issue - State: closed - Opened by messersc almost 6 years ago - 1 comment

#6 - Gh pages update

Pull Request - State: closed - Opened by christianholland over 6 years ago
Labels: update

#5 - Add function to test for differences between conditions

Issue - State: closed - Opened by mschubert almost 7 years ago
Labels: enhancement

#4 - Provide means of scaling by control

Issue - State: closed - Opened by mschubert almost 7 years ago
Labels: enhancement

#3 - Provide pre-calculated GDSC/TCGA scaling

Issue - State: closed - Opened by mschubert almost 7 years ago
Labels: enhancement

#2 - Potentially include utility functions for other pathway methods

Issue - State: closed - Opened by mschubert about 8 years ago
Labels: enhancement

#1 - Warn/error if unable to match HGNC symbols

Issue - State: closed - Opened by mschubert about 8 years ago
Labels: enhancement

GitHub / saezlab/progeny issues and pull requests