martinjzhang/scDRS issues and pull requests

#104 - Sig. cell type-disease associations and Sig. individual cells

Issue - State: closed - Opened by hopehan12 17 days ago - 3 comments

#103 - About the H5AD input - raw counts or normalized+transformed?

Issue - State: closed - Opened by hopehan12 22 days ago - 2 comments

#102 - Why are some of the CORR columns in the <trait>.scdrs_gene file negative, and the largest RANK level is the smallest negative number, can this represent the gene most associated with disease and cell type?

Issue - State: closed - Opened by MoWeiLanChen 23 days ago - 1 comment

#101 - scdrs perform-downstream: fail to load scDRS full score gz file

Issue - State: closed - Opened by hopehan12 about 1 month ago - 2 comments

#100 - Questions about reproducing results

Issue - State: closed - Opened by HelloWorldLTY about 1 month ago - 10 comments

#99 - The relationship between cell type association and heterogeneity

Issue - State: open - Opened by AI-10 about 2 months ago

#98 - Questions about example dataset usage

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

#97 - Issue with plot using scdrs.util.plot_group_stats

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

#96 - Update index.rst to fix a bug in the installation process

Pull Request - State: closed - Opened by HelloWorldLTY about 2 months ago - 2 comments

#95 - Questions about matched gene sets

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

#94 - Correcting cell-level p-values for multiple comparisons?

Issue - State: open - Opened by schroeme about 2 months ago - 3 comments

#93 - fail to get the "1000 top associated genes" based on MAGMA

Issue - State: closed - Opened by yihancc 2 months ago - 2 comments

#92 - use scdrs in a tissue seemlingly unrelated with the disease

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

#91 - tcell.facs.annot.h5ad without GENE name

Issue - State: closed - Opened by Davidseye 3 months ago - 2 comments

#90 - Preprocessing: killed running scdrs compute-score

Issue - State: closed - Opened by schroeme 4 months ago - 4 comments

#89 - Converting GWAS catalog .tsv file to gene set

Issue - State: closed - Opened by kayihui 4 months ago - 3 comments

#88 - ValueError: too many values to unpack (expected 2)

Issue - State: closed - Opened by kayihui 4 months ago - 8 comments

#87 - Using geneset from SMR result

Issue - State: closed - Opened by Misaka-15134 4 months ago - 1 comment

#86 - Interpreting scDRS score when comparing cell-type subclusters

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

#85 - Issue83

Pull Request - State: closed - Opened by martinjzhang 5 months ago

#84 - The 'n_fdr_0.2' number of all group is 0

Issue - State: closed - Opened by Y-Isaac 5 months ago - 7 comments

#83 - AssertionError when running quick test after installation

Issue - State: closed - Opened by hoholee 6 months ago - 7 comments

#82 - trait=z_score: skipped due to small size (n_gene=5, sys_time=116.1s)

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

#81 - TypeError: plot_group_stats() got an unexpected keyword argument 'plot_kws'

Issue - State: closed - Opened by Huiflorazhan 8 months ago - 16 comments

#80 - Is it reasonable to use human' geneset on mouse scRNAseq data?

Issue - State: closed - Opened by zehualilab 8 months ago - 2 comments

#79 - About compute-score

Issue - State: closed - Opened by evenDDDDD 8 months ago

#78 - TypeError: '<' not supported between instances of 'str' and 'float'

Issue - State: closed - Opened by zehualilab 9 months ago - 3 comments

#77 - Subsetting cells for downstream analysis.

Issue - State: closed - Opened by jeji0209 10 months ago - 1 comment

#76 - fixed the bug in scdrs/util.py

Pull Request - State: closed - Opened by yyoshiaki 10 months ago - 2 comments

#75 - add option for specifying FDR threshold in plot_group_stats

Pull Request - State: closed - Opened by KangchengHou 11 months ago - 3 comments

#74 - The graphs from a single result and multiple results are inconsistent

Issue - State: closed - Opened by QianChwnLyn 11 months ago - 13 comments

#73 - custom gene set ?

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

#72 - compute-score is not reading .gs file properly

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

#71 - Gene weights or without gene weights

Issue - State: closed - Opened by QianChwnLyn 12 months ago - 3 comments

#70 - Update dependencies of scDRS

Issue - State: open - Opened by martinjzhang about 1 year ago
Labels: bug

#69 - gene weights for the control genes

Issue - State: closed - Opened by aandreas13 about 1 year ago - 5 comments

#68 - Issues Plotting UMAP from quick start tutorial

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

#67 - error metaclass conflict

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

#66 - turning off fdr correction

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

#65 - plot_group_stats() got an unexpected keyword argument 'plot_kws'

Issue - State: closed - Opened by milospjanic over 1 year ago - 15 comments

#64 - perform-downstream outputs zero significant cells

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

#63 - scRNA data input

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

#62 - Error in scdrs perform-downstream --group-analysis

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

#61 - munge-gs input format

Issue - State: closed - Opened by DonaldSandoz2000 over 1 year ago - 2 comments

#60 - Remove NA values in corr anlaysis

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

#59 - Convert Seurat object to h5ad file

Issue - State: open - Opened by uqzqiao over 1 year ago - 19 comments

#58 - update doc: clatify raw p-val; procedure to increase MC samples in gr…

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

#57 - scdrs compute-score output

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

#56 - Please help with scDRS for the plant Arabidopsis thaliana

Issue - State: closed - Opened by bitcometz over 1 year ago - 15 comments

#55 - Update compute_magma_gs.md

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

#54 - "skipped due to small size" error

Issue - State: closed - Opened by NaomiHuntley over 1 year ago - 9 comments

#53 - Issue52

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

#52 - Error when adata.obs_names can be interpreted as integers

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

#51 - Considerations for single cell splicing data

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

#50 - tutorial-Quick start ——full_score.gz

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

#49 - GWAS traits and a control traits

Issue - State: closed - Opened by Li-mengjie almost 2 years ago - 12 comments

#48 - Adjusting for donor effects

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

#47 - Multiple testing correction on downstream analysis

Issue - State: closed - Opened by aandreas13 almost 2 years ago - 2 comments

#46 - compute-score can not complete

Issue - State: closed - Opened by Dan-121 almost 2 years ago - 7 comments

#45 - scdrs CLI not working?

Issue - State: closed - Opened by Dzhan4 almost 2 years ago - 3 comments

#44 - Seurat to h5ad

Issue - State: closed - Opened by Dzhan4 almost 2 years ago - 7 comments

#43 - Cell-type disease association vs proportion of significant cells

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

#42 - concerning beta or OR when choosing putative disease genes

Issue - State: open - Opened by parkjooyoung99 almost 2 years ago - 1 comment

#41 - check input in munge-gs

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

#40 - munge-gs type error

Issue - State: closed - Opened by parkjooyoung99 almost 2 years ago - 2 comments

#39 - Negative weights in munge-gs

Issue - State: open - Opened by martinjzhang almost 2 years ago

#38 - Issues with generating gs files

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

#37 - Problem with munging

Issue - State: closed - Opened by HJ234 about 2 years ago - 6 comments

#36 - Adding arguments of min_cells and min_genes to CLI for data filtering

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

#35 - Issue32

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

#34 - Print cell type info

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

#33 - Segmentation fault when Running scDRS

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

#32 - Data sparsity is a critical problem for the inference stability (ex. 10x data)

Issue - State: closed - Opened by yyoshiaki about 2 years ago - 11 comments
Labels: enhancement, good first issue, question

#31 - scDRS CLI scdrs munge-gs

Issue - State: closed - Opened by Alina-Song about 2 years ago - 1 comment

#30 - Broader control gene sets

Issue - State: open - Opened by kitscorp about 2 years ago - 1 comment
Labels: enhancement, question

#29 - Problems with input data

Issue - State: closed - Opened by Mia1037 about 2 years ago - 6 comments
Labels: documentation, question

#28 - doc v1.0.2

Pull Request - State: closed - Opened by martinjzhang about 2 years ago

#27 - Drop duplicates for pval_file and zsc_file

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

#26 - Check inputs

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

#25 - Loess error in compute-score after subsampling

Issue - State: closed - Opened by twoneu about 2 years ago - 5 comments

#24 - KeyError: at plot_group_stats step

Issue - State: closed - Opened by twoneu about 2 years ago - 12 comments
Labels: bug

#23 - scDRS breaks if using all scRNA-seq genes as disease genes

Issue - State: open - Opened by martinjzhang about 2 years ago
Labels: enhancement

#22 - cope with categorical covariates

Pull Request - State: closed - Opened by KangchengHou about 2 years ago

#21 - Accept categorical covariates

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

#20 - Ordinal covariates

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

#19 - Cleaning/prepping GWAS statistics

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

#18 - Tutorial for preparing files

Issue - State: closed - Opened by martinjzhang over 2 years ago

#17 - MC-z and MC-z-based p-value

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

#16 - Correct ctp

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

#15 - Test cli

Pull Request - State: closed - Opened by martinjzhang almost 3 years ago - 2 comments