Ecosyste.ms: Issues

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GitHub / neurogenomics/magma_celltyping issues and pull requests

#157 - MAGMA.Celltyping::get_example_gwas() error

Issue - State: closed - Opened by Jadeapple 3 months ago - 6 comments
Labels: bug

#156 - ERROR - reading gene covariate file: duplicate variable name 'Fetal_Neuron'

Issue - State: closed - Opened by bschilder 4 months ago - 6 comments
Labels: bug

#155 - Test auto-close

Issue - State: closed - Opened by bschilder 5 months ago
Labels: bug

#154 - Issue downloading & unzipping reference files for MAGMA run

Issue - State: closed - Opened by Al-Murphy 5 months ago - 3 comments
Labels: bug

#153 - How to use GWAS results from studies not included in this package

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

#152 - map_snps_to_genes

Issue - State: closed - Opened by ushagogal 7 months ago - 1 comment
Labels: bug

#150 - Update MAGMA file links

Issue - State: closed - Opened by bschilder 9 months ago
Labels: bug

#149 - map_snps_to_genes() and get_ctd() related errors

Issue - State: closed - Opened by zsf123525 12 months ago - 1 comment
Labels: bug

#148 - Magma used in other species

Issue - State: closed - Opened by sanderslhc over 1 year ago - 1 comment
Labels: invalid

#147 - found 0 valid gene covariates, for 0 genes defined in genotype data

Issue - State: closed - Opened by sanderslhc over 1 year ago - 11 comments
Labels: bug, invalid

#146 - too many correlations

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

#145 - map_snps_to_genes() related error

Issue - State: open - Opened by barbareyex over 1 year ago - 5 comments
Labels: bug

#144 - `map_snps_to_genes`: Handle bgzipped files

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

#143 - Assess whether MAGMA can take multi-allelic SNPs

Issue - State: closed - Opened by bschilder almost 2 years ago - 13 comments
Labels: enhancement, documentation

#142 - ERROR - reading gene covariate file: duplicate covariate variable name

Issue - State: closed - Opened by bschilder almost 2 years ago - 3 comments
Labels: bug

#141 - *gsa.out: truncated `VARIABLE` names

Issue - State: closed - Opened by bschilder almost 2 years ago - 1 comment
Labels: bug

#140 - get_ctd doesn't work - "missing token error"

Issue - State: closed - Opened by the-confused-scientist almost 2 years ago - 1 comment
Labels: bug

#139 - `\doi{}` tag not rendering properly

Issue - State: closed - Opened by bschilder almost 2 years ago
Labels: bug, documentation

#138 - Add full AIBS data from all regions

Issue - State: closed - Opened by bschilder almost 2 years ago - 1 comment
Labels: enhancement

#137 - MAGMA.Celltyping::import_magma_files issue

Issue - State: open - Opened by sofiapuvogelvittini about 2 years ago - 1 comment
Labels: bug

#136 - Unable to import the example GWAS summary statistics when MUNGE = FALSE

Issue - State: open - Opened by Sheenlei about 2 years ago - 1 comment
Labels: bug

#135 - Fix top10 condition analysis

Pull Request - State: closed - Opened by AMCalejandro over 2 years ago - 3 comments

#134 - Maybe allow user to decide on how to adjust

Issue - State: open - Opened by AMCalejandro over 2 years ago - 2 comments
Labels: enhancement

#133 - Fix get_data gh

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

#132 - Fix adding full method to results

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

#131 - Almost all CTDs are not available

Issue - State: closed - Opened by AMCalejandro over 2 years ago - 3 comments
Labels: bug

#130 - Problem with zeisel 2018 ctd

Issue - State: closed - Opened by KittyMurphy over 2 years ago - 1 comment
Labels: bug

#129 - ERROR - configuration: unknown modifier 'twosided' for flag --set-annot

Issue - State: closed - Opened by AMCalejandro over 2 years ago - 1 comment
Labels: bug

#128 - Bug report:Error in if (is.null(N) | is.na(N)) { : argument is of length zero

Issue - State: closed - Opened by ZhengGongwei over 2 years ago - 4 comments
Labels: bug

#127 - Likely bug if dendro is set to Null

Issue - State: closed - Opened by AMCalejandro over 2 years ago - 1 comment
Labels: bug

#126 - magma_tileplot does not overlap the dendrogram with the heatmap

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

#125 - WARNING: 228 columns (cell-types) have less than the expected number of quantile bins (10).

Issue - State: closed - Opened by AMCalejandro over 2 years ago - 1 comment
Labels: bug

#124 - Unable to pass path to refen

Issue - State: open - Opened by AMCalejandro over 2 years ago
Labels: bug

#123 - Overadjustment for multiple testing?

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

#122 - Issue in EWCE if I leave MAGMA.Celltyping calculate the quantiles

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

#121 - `plot_celltype_associations`: Fix adding full method to results

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

#120 - Fix GH Actions

Issue - State: closed - Opened by bschilder over 2 years ago - 2 comments
Labels: bug, GitHub Actions

#119 - Create CTDs from `scRNAseq` package datasets

Issue - State: open - Opened by bschilder over 2 years ago
Labels: enhancement

#118 - Upload Zeisel2018 CTD

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

#116 - `get_driver_genes`: select genes by mean rank

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

#115 - `merge_results`: create`save_dir` if not already present

Issue - State: closed - Opened by bschilder over 2 years ago
Labels: bug

#114 - Use `adjust_zstat_in_genesOut` without a CTD

Issue - State: closed - Opened by bschilder over 2 years ago - 1 comment
Labels: enhancement

#111 - Update `full_workflow` vignette to work

Issue - State: closed - Opened by bschilder over 2 years ago
Labels: bug

#110 - Parallelise MAGMA steps

Issue - State: open - Opened by bschilder over 2 years ago - 1 comment
Labels: enhancement

#109 - Add functions to import genes.out and genes.raw files into R

Issue - State: closed - Opened by bschilder over 2 years ago - 2 comments
Labels: enhancement, help wanted

#108 - `map_snps_to_genes`: Add *--genes-only* arg

Issue - State: closed - Opened by bschilder over 2 years ago - 1 comment
Labels: enhancement

#107 - Error running after using new version of .rds files

Issue - State: closed - Opened by Captain-Pam over 2 years ago - 4 comments
Labels: bug

#106 - `get_ctd`:`Error in gzfile(file) : invalid 'description' argument`

Issue - State: closed - Opened by bschilder over 2 years ago
Labels: bug

#105 - Error in "map_snps_to_genes"

Issue - State: closed - Opened by LDHHAHA almost 3 years ago - 8 comments
Labels: bug

#104 - Add Tabula Muris

Issue - State: closed - Opened by bschilder almost 3 years ago
Labels: enhancement

#103 - MAGMA_Files_Public studies identification

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

#102 - get_genomeLocFile() issue

Issue - State: closed - Opened by shivani-raja almost 3 years ago - 8 comments
Labels: bug

#101 - Problem with get_genomeLocFile

Issue - State: closed - Opened by malosreet about 3 years ago - 1 comment

#100 - get_genomeLocFile error

Issue - State: closed - Opened by malosreet about 3 years ago - 6 comments

#99 - time out 300s

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

#98 - Installation failed

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

#97 - cell type data no longer compatible with EWCE

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

#96 - Compare `MAGMA.Celltyping` v1.0 vs. v2.0

Issue - State: closed - Opened by bschilder about 3 years ago

#95 - Increase test coverage

Issue - State: closed - Opened by bschilder about 3 years ago - 9 comments
Labels: enhancement

#94 - Remove EWCE from Remotes

Issue - State: closed - Opened by bschilder about 3 years ago

#93 - `MAGMA.Celltyping`: bschilder_dev upgrade

Pull Request - State: closed - Opened by bschilder about 3 years ago - 3 comments
Labels: bug, enhancement

#92 - Get MAGMA.Celltyping working on Windows

Issue - State: closed - Opened by bschilder about 3 years ago
Labels: bug

#91 - map.snps.to.genes: Error in strsplit(first_line, "\t") : non-character argument

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

#90 - Use stored URLs for MAGMA_Files_Public

Issue - State: closed - Opened by bschilder about 3 years ago

#89 - Provide built-in links to MAGMA binaries

Issue - State: closed - Opened by bschilder about 3 years ago

#88 - Provide built-in MAGMA files

Issue - State: closed - Opened by bschilder about 3 years ago

#88 - Provide built-in MAGMA files

Issue - State: closed - Opened by bschilder about 3 years ago

#87 - Create hex sticker

Issue - State: closed - Opened by bschilder about 3 years ago - 1 comment

#86 - New function: `get_sub_SNP_LOC_DATA()`

Issue - State: closed - Opened by bschilder about 3 years ago - 1 comment

#85 - Move gene coordinate files

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

#84 - Avoid `format.sumstats.for.magma` being interpreted as an S3 method

Issue - State: closed - Opened by bschilder about 3 years ago - 1 comment

#83 - Pass CRAN checks

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

#83 - Pass CRAN checks

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

#82 - `Warning: ...storing paths of more than 100 bytes is not portable:`

Issue - State: closed - Opened by bschilder about 3 years ago - 1 comment

#81 - Print user-friendly magma commands

Issue - State: closed - Opened by bschilder about 3 years ago

#80 - Remove `genome_ref_path` as requirement for `calculate_celltype_associations`

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

#79 - Remove `reshape` dependency

Issue - State: closed - Opened by bschilder about 3 years ago

#78 - `calculate_conditional_geneset_enrichment`: Handle different versions of MAGMA

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

#77 - Add unit tests

Issue - State: closed - Opened by bschilder about 3 years ago

#76 - Benchmark `orthogene::all_genes` vs. `hgnc2entrez`

Issue - State: closed - Opened by bschilder about 3 years ago - 1 comment

#75 - Deprecate functions

Issue - State: closed - Opened by bschilder about 3 years ago

#74 - Remove `cowplot` dependency

Issue - State: closed - Opened by bschilder about 3 years ago

#73 - Create MAGMA files repository

Issue - State: closed - Opened by bschilder about 3 years ago - 1 comment

#72 - Remove `library` calls within code

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

#71 - Make code human-readable

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

#70 - Use `#### header ####` in comments

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

#69 - Add both `@title` and `@description` to all Roxygen notes

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

#68 - Make function arguments explicit

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

#67 - Replace all usage of `1:10` syntax

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

#66 - Remove `suppressWarnings` calls

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

#65 - Add function links to Roxygen notes

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

#64 - Make function argument names consistent

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

#63 - Replace "." with "_" in function names

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

#62 - Provide working `@examples`

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

#61 - Remove `usethis` calls from uncommented code

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

#60 - Avoid accidentally renaming columns

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