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Al-Murphy
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MungeSumstats
Rapid standardisation and quality control of GWAS or QTL summary statistics
https://doi.org/doi:10.18129/B9.bioc.MungeSumstats
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Column name handling: Freq vs . MAF
#95
bschilder
closed
2 years ago
4
Additional CHR synonyms
#94
bschilder
closed
2 years ago
1
Cache liftover chain files
#93
bschilder
closed
2 years ago
3
Create shell wrapper
#92
bschilder
opened
2 years ago
0
`get_genome_build`: Can't find SNP, CHR, BP in PGC VCFs
#91
bschilder
closed
2 years ago
5
GitHub Pages Documentation site missing
#90
mkoromina
closed
2 years ago
3
Some SNP RS IDs were wrongly imputed.
#89
Huifang-Xu
closed
2 years ago
7
Odds ratio (OR) shouldn’t be negative value when flipping effect allele
#88
Huifang-Xu
closed
2 years ago
4
PR: Impute Beta & SE
#87
Al-Murphy
closed
2 years ago
0
PR: Impute Beta & SE
#86
Al-Murphy
closed
2 years ago
0
Calculate effect columns when missing
#85
Al-Murphy
closed
2 years ago
1
error in get_chian_file.R
#84
Cloufield
closed
2 years ago
6
Error in .new_IRanges_from_start_end(start, end) : 'start' or 'end' cannot contain NAs
#83
albert-ying
closed
2 years ago
8
Cant access the output
#82
soren-rand
closed
2 years ago
5
Non-biallelic SNPs shouldn't be checked for dups based on RSID alone
#81
Al-Murphy
closed
2 years ago
1
Avoid appending old log files
#80
bschilder
opened
2 years ago
4
`Error: Default branch mismatch between local repo and remote.`
#79
bschilder
closed
2 years ago
1
GHA failing tests fails on WIndows: `index_tabix`?
#78
bschilder
closed
2 years ago
1
Extend quality control and standardisation to QTL analysis
#77
Al-Murphy
opened
2 years ago
2
p-values > 1
#76
bschilder
closed
2 years ago
3
ukb-b-14043: 0 variants remaining
#75
bschilder
closed
2 years ago
3
`import_sumstats`: Avoid downloading VCF when munged sum stats already exist
#74
bschilder
closed
2 years ago
1
Bschilder dev
#73
bschilder
closed
2 years ago
2
Add Docker vignette
#72
bschilder
closed
2 years ago
0
Update GHA workflows
#71
bschilder
closed
2 years ago
0
Add example log file
#70
bschilder
closed
2 years ago
0
Add helper function to search for previous munged sumstats
#69
bschilder
closed
2 years ago
1
Add function to parse logs
#68
bschilder
closed
2 years ago
2
Differentiate between errors and restricted datasets
#67
bschilder
opened
2 years ago
5
`import_sumstats`: Save each GWAS as a directory with respective log files
#66
bschilder
closed
2 years ago
1
Make data.table `nThread=1` explicit in tests
#65
bschilder
closed
3 years ago
0
Handle reading .bgz files
#64
bschilder
closed
3 years ago
0
Read VCFs without #CHR
#63
bschilder
closed
3 years ago
2
Check that save_path dir exists early on
#62
bschilder
closed
3 years ago
0
Messages don't print when recording logs
#61
bschilder
closed
3 years ago
2
`test-IEU_GWAS` not passing
#60
bschilder
closed
3 years ago
1
Add tests for `get_genome_builds`
#59
bschilder
closed
3 years ago
3
VCF enhancements
#58
Al-Murphy
closed
3 years ago
6
`Incompatible join types: x.BP (character) and i.BP (integer)`
#57
bschilder
closed
3 years ago
3
`read_vcf`: `Error in file(file, "wb") : cannot open the connection`
#56
bschilder
closed
3 years ago
3
`path` argument not used in `standardise_sumstats_column_headers_crossplatform`
#55
bschilder
closed
3 years ago
1
Speed up `get_genome_build`
#54
bschilder
closed
3 years ago
3
`Error in startsWith(path, "https://gwas.mrcieu.ac.uk")`
#53
bschilder
closed
3 years ago
3
Add "N" to `find_sumstats` table
#52
bschilder
closed
3 years ago
0
`object 'UKB-b:323' not found`
#51
bschilder
closed
3 years ago
1
Provide liftover to other genome builds
#50
bschilder
closed
3 years ago
5
`missing value where TRUE/FALSE needed`
#49
bschilder
closed
3 years ago
13
Miscellaneous errors encountered when parsing summary stats
#48
demodw
closed
3 years ago
6
Update Bioconductor binaries?
#47
demodw
closed
3 years ago
2
`allele_flip_frq = T` gives negative `FRQ` instead of `1 - FRQ` when flipped
#46
albert-ying
closed
3 years ago
1
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