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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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`format_sumstats` doesn't detect lowercase alleles (with fix)
#145
HaglundA
closed
1 year ago
2
Error in .start_as_unnamed_integer(start) : each range must have a start that is < 2^31 and > - 2^31
#144
1650783167jyw
closed
1 year ago
7
Non-European populations
#143
irisjansen
closed
1 year ago
3
Updating column headers - new mapping not working with format_sumstats()?
#142
aepacker
closed
1 year ago
4
Tag releases for improved reproducibility when installing MSS in Docker containers
#141
jksull
closed
1 year ago
2
SNPs not found on reference when using (default)`flip_check` even though they do exist
#140
jksull
closed
1 year ago
6
Unclear why SNPs are not chosen for validation
#139
jksull
closed
1 year ago
6
MungeSumstats appears to be flipping alleles (and with it the `beta` and `FRQ`'s) when it shouldn't
#138
jksull
closed
1 year ago
13
Problem in running MungeSumstats::format_sumstats with bi_allelic_filter = FALSE
#137
rootze
closed
1 year ago
2
could not find function "liftover"
#136
ElizavetaElgaeva
closed
1 year ago
3
impute_beta appears to be not an argument
#135
irisjansen
closed
1 year ago
4
`format_sumstats` cannot differentiate `\t` and `whitespace` when used together
#134
Lloyd-LiuSiyi
closed
1 year ago
2
Allow use of Ensembl chain
#133
jonathangriffiths
closed
1 year ago
1
Connectome Vignette comments
#132
Al-Murphy
closed
1 year ago
1
Take name from input data and use it to save the logs
#131
AMCalejandro
closed
1 year ago
5
Clarity needed for the treatment of sex chromosomes
#130
LeiSunUofT
closed
1 year ago
3
ES and beta imputation
#129
BEFH
closed
2 years ago
11
Update chain files due to licensing
#128
Al-Murphy
closed
1 year ago
2
Error in data.table::fwrite zlib library
#127
manuelatan
closed
2 years ago
5
Fix NA representation for tabular outputs
#126
BEFH
closed
2 years ago
0
`compute_nsize`: handle a vector of sample sizes
#125
bschilder
closed
2 years ago
3
Many non biallelic variants get removed
#124
AMCalejandro
closed
2 years ago
1
Error in ids2rowids(ids) : cannot extract the digital part of some SNP ids in 'ids'
#123
AMCalejandro
closed
2 years ago
1
Replace `seqminer`
#122
bschilder
closed
2 years ago
1
Extra .tsv after tabix indexing
#121
bschilder
closed
2 years ago
0
Error in split out chr:bp (check_no_rs_snp)
#120
abigailterkuile
closed
2 years ago
4
Can't assign to the same column twice in the same query (duplicates detected)
#119
PhoebeGuo97
closed
2 years ago
1
Is function "liftover" available in R package?
#118
RuochengDong
closed
2 years ago
2
Create tabix index failed
#117
PhoebeGuo97
closed
1 year ago
38
MT chromosome value converted to NA
#116
ilevantis
closed
2 years ago
1
How can I get N column for the subsequent ldsc analysis?
#115
zh-zhang1984
closed
2 years ago
4
validate_parameters checks for incorrect version of dbSNP package
#114
ilevantis
closed
2 years ago
1
`cannot find an open port. For manually specifying the port, see ?SnowParamUsing previously downloaded VCF.`
#113
bschilder
opened
2 years ago
1
Munging full summary stats is slow
#112
PhoebeGuo97
closed
2 years ago
3
Large number of non-biallelic SNPs
#111
bschilder
closed
2 months ago
15
format_sumstats error "Can't assign to the same column twice in the same query (duplicates detected)"
#110
kisudsoe
closed
2 years ago
6
`find_sumstats()`: N column in metadata
#109
bschilder
closed
2 years ago
3
High percentage of A1 not matching the reference genome
#108
lpgilchrist
closed
2 years ago
2
`Could not recognize genome build of: - target_genome`
#107
bschilder
closed
2 years ago
2
Elimination of Chromosome and base position turns pvalues to NA
#106
fernandogs97
closed
2 years ago
1
how to calculate EAF from FRQ_A and FRQ_U?
#105
showers14
closed
2 years ago
2
Incorrect CHR assignment after liftover
#104
quattro
closed
2 years ago
6
GenomicRanges style update broken for X chromosome
#103
quattro
closed
2 years ago
4
VCF output which conforms GWAS-VCF specification
#102
ilevantis
closed
2 years ago
3
Update `compute_nsize` docs
#101
bschilder
closed
2 years ago
1
Accidentally assigning AF as INFO
#100
bschilder
closed
2 years ago
3
Posthuma2021 GWAS
#99
bschilder
closed
2 years ago
10
Update dbSNP references when available on Bioconductor
#98
Al-Murphy
closed
2 years ago
6
Column name handling: "NGT"
#97
bschilder
closed
2 years ago
3
Column name handling: start/end
#96
bschilder
opened
2 years ago
8
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