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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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Set default to keep non-bi-allelic SNPs
#196
Al-Murphy
opened
3 weeks ago
0
different gwas column title to import
#195
songlyzz
closed
1 month ago
1
Add FAQ of common queries to documentation
#194
Al-Murphy
closed
3 weeks ago
0
Add parameter for assuming minor allele is the effect allele
#193
Al-Murphy
closed
1 month ago
13
Add to mapping file risk non-risk alleles
#192
Al-Murphy
closed
2 months ago
1
Add functionality to MungeSumstats so users can supply tarball of differing dbSNP versions
#191
Al-Murphy
opened
2 months ago
0
MungeSumstats on GWAS data from non-Europeans
#190
MC4R
closed
3 months ago
3
Inquiry on Converting MAF to EAF Using MungeSumstats
#189
DaXuanGarden
closed
1 week ago
2
Allele flip seems not work
#188
htqqdd
closed
1 week ago
4
ValueError: Improperly formatted sumstats file:
#187
AndreaG5
closed
4 months ago
2
`format_sumstats()` duplicates base letter between `A1` and `A2`
#186
rmgpanw
closed
6 months ago
1
liftover not working for certain region
#185
zhana-optima
closed
6 months ago
3
Enhancement for liftover function
#184
laleoarrow
closed
7 months ago
1
Add local chain file option for MungeSumstats::liftover # enhancement
#183
laleoarrow
closed
7 months ago
1
add `drop_na_cols` parameter to `format_sumstats()`
#182
rmgpanw
closed
7 months ago
3
`format_sumstats()` removes rows with unneeded columns that contain `NA` values
#181
rmgpanw
closed
7 months ago
2
All SNPs have been filtered out of your summary statistics dataset
#180
TullyMonster
closed
7 months ago
6
Check Position by rsID rather than updating the rsID?
#179
erikstricker
closed
8 months ago
2
Requires BRug which is only working on R 4.2 or older
#178
erikstricker
closed
8 months ago
5
Error in `sort_coords()` due to `NA` in columns `CHR` & `BP`
#177
cfbeuchel
closed
9 months ago
3
Error in `check_no_rs_snp()` when joining with duplicate key values
#176
cfbeuchel
closed
9 months ago
3
Add checks to standardise_sumstats_column_headers_crossplatform()
#175
cfbeuchel
closed
9 months ago
0
Patch standardise sumstats column headers crossplatform (+QOL improvements)
#174
cfbeuchel
closed
9 months ago
2
Fix bug in standardise_sumstats_column_headers_crossplatform
#173
cfbeuchel
closed
9 months ago
2
How to load local chain files
#172
sfgfdasd
closed
10 months ago
6
dbSNP154
#171
AhmedArslan
closed
3 months ago
2
Fix GitHub Action
#170
bschilder
opened
1 year ago
8
Finding manual of previous versions
#169
jksull
closed
3 months ago
4
Update header mappings
#168
mykmal
closed
1 year ago
7
SNPlocs.Hsapiens.dbSNP156.GRCh37
#167
AndyYang0924
closed
2 months ago
5
Fix bug for no indels
#166
jonathangriffiths
closed
1 year ago
1
Allele frequency cant be flipped for multi-allelic variants.
#165
kousathanas
closed
1 year ago
4
Join results in more than 2^31 rows for format_sumstats
#164
Snigireva
opened
1 year ago
3
Error in `[.data.table`(sumstats_dt, rsids, `:=`(SNP, i.RefSNP_id)) : 当删除列时，不应指定 i
#163
x-level
closed
1 year ago
8
Crash when imputation_ind = TRUE and chr:bp identifiers are present
#162
mykmal
closed
1 year ago
1
format_sumstats() does not check column type
#161
rmgpanw
closed
1 year ago
3
Option to specify effect allele as A1 instead.
#160
svenkatesh25
closed
3 months ago
16
Crash due to missing IMPUTATION_SNP column
#159
mykmal
closed
1 year ago
2
Add support for alternative chromosome styles
#158
mykmal
closed
1 year ago
1
Improve chromosome standardization
#157
mykmal
closed
1 year ago
4
fix for bug #155: inappropriate detection of vcf file
#156
BEFH
closed
1 year ago
1
`read_sumstats()` detects a vcf file if "vcf" is anywhere in the file path except the beginning.
#155
BEFH
closed
1 year ago
0
[E::hts_idx_push] Unsorted positions on sequence #1
#154
maryellenlynall
closed
1 year ago
2
`format_sumstats()` fails to infer genome build
#153
mykmal
closed
1 year ago
2
Effect allele A1 or A2?
#152
anbai106
closed
1 year ago
3
save_format error
#151
adannasusan
closed
1 year ago
2
`NA` values lead to `rbindlist` error when `imputation_ind = TRUE`
#150
JustinCope
closed
1 year ago
1
format_sumstats p value column selection problem
#149
dupontct
closed
1 year ago
2
sumstatsColHeaders duplicates
#148
svenkatesh25
closed
1 year ago
2
Error: 'formatted_example' is not an exported object from 'namespace:MungeSumstats'
#147
chenyangjjj
closed
1 year ago
2
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