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neurogenomics
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MAGMA_Celltyping
Find causal cell-types underlying complex trait genetics
https://neurogenomics.github.io/MAGMA_Celltyping
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Run `prepare_quantile_groups` internally
#56
bschilder
closed
2 years ago
0
Make upstream_kb/downstream_kb defaults
#55
bschilder
closed
2 years ago
0
Allow the use of non-European populations
#54
bschilder
closed
2 years ago
0
Replace genome_ref file with Bioconductor data
#53
bschilder
opened
2 years ago
2
Make it so the geneset enrichment function can screen all GO gene sets
#52
NathanSkene
opened
3 years ago
0
Setup pkgdown for the documentation so users can see either the short or full vignette
#51
NathanSkene
closed
2 years ago
1
Enable any species to be specified for the CTD & remove explicit checks or MGI/HGNC
#50
NathanSkene
closed
2 years ago
1
Check how automated install options for magma behave on various operating systems & HPC & Travis & GithubActions
#49
NathanSkene
closed
2 years ago
2
Confirm that all functions work with the latest version of magma (1.09b) and if not force dependency on older version
#48
NathanSkene
closed
2 years ago
2
Enable build tests + unit tests to work on travis / github actions, despite the dependancy on external magma executable
#47
NathanSkene
closed
2 years ago
2
Try to reduce the size of example sumstats files to 30mb
#46
NathanSkene
closed
2 years ago
2
map.snps.to.genes error: object 'read_header' not found
#45
ChenJin2020
closed
3 years ago
1
magma: /lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by magma)
#44
stergiostsartsalis
closed
3 years ago
2
Update MungeSumstats reference to bioconductor version when live
#43
Al-Murphy
closed
3 years ago
1
error while processing mouse data
#42
kvshams
closed
3 years ago
5
"There is no SNP column found within the data." Error in load(filePath) : empty (zero-byte) input file
#41
acburns
closed
3 years ago
30
Add functions to find intersection of genes with high genetic load + cell type specificity (similar to approach used in Parkinsons nature genetics paper)
#40
williamlam314
closed
2 years ago
3
enrichment_p or P?
#39
zhanglab2008
closed
3 years ago
1
Bschilder dev
#38
bschilder
closed
3 years ago
0
Support multiple threads or not?
#37
Shicheng-Guo
closed
3 years ago
1
Does MAGMA_Celltyping regenerate quantiles, even when EWCE has already generated them, and then save them to a new location?
#36
NathanSkene
closed
2 years ago
2
Add an error catch to prepare.quantile.groups
#35
NathanSkene
closed
2 years ago
3
Handling other matrix types
#34
bschilder
closed
3 years ago
1
Error in if (genome_build == "GRCh37") { : argument is of length zero
#33
atulkumar1301
closed
3 years ago
4
Add code to generate tile plots for a set of GWAS, with num genome-wide signif loci displayed above, with neat X-axis labels, using IEUGWAS to import details for the labels
#32
montenegrina
opened
3 years ago
4
Add interface to IEU Open GWAS R Package as alternative to formatting sumstats etc
#31
NathanSkene
closed
2 years ago
2
Add functionality to allow magma files to be used when full sumstats no longer available
#30
NathanSkene
closed
2 years ago
1
Add R function to help install magma command line tool
#29
bschilder
closed
2 years ago
4
`Error in if (genome_build == "GRCh37") { : argument is of length zero`
#28
bschilder
closed
3 years ago
14
Missing function `format_sumstats_for_magma_crossplatform()`
#27
bschilder
closed
3 years ago
4
The genomeLocFile now directs to /path/to/MAGMA.Celltyping/data//NCBI*
#26
NathanSkene
closed
2 years ago
1
Devtools checking
#25
NathanSkene
closed
4 years ago
0
Dev
#24
NathanSkene
closed
4 years ago
0
error: magma does not appear to be located on your path
#23
yabwei
closed
3 years ago
5
Magma celltyping on snATAC data
#22
prashanthsama1
closed
3 years ago
1
Installation Error: package ‘EWCE’ could not be loaded
#21
prashanthsama1
closed
4 years ago
5
Add functions for testing a whole set of traits in one go + multiple correction testing for them + generating plots
#20
kvshams
closed
2 years ago
1
Identifying the gene load
#19
kvshams
closed
3 years ago
1
Typo fixed on paragraph 176
#18
kant
closed
4 years ago
0
Minor fixes on line 176 & paragraph 96
#17
kant
closed
2 years ago
1
Add function to create plot showing enrichment with error bars at each decile
#16
NathanSkene
opened
4 years ago
1
Added N argument and removed questions for user input in the format_sumstats_for_magma function
#15
KristinaSalontaji
closed
3 years ago
1
Going through the example
#14
galvaniquee
closed
4 years ago
3
Fix issues in loading results and plotting
#13
zj-liu
closed
3 years ago
0
Checking labelling of "-log10 P-value" on plot x-axis
#12
krademaker
closed
2 years ago
1
plot_celltype_associations using old 'quantiles' variable
#11
krademaker
closed
5 years ago
2
Two issues about reading MAGMA output and ploting
#10
zj-liu
closed
5 years ago
0
Bug in check_inputs_to_magma_celltype_analysis
#9
alexandruioanvoda
closed
5 years ago
3
numberOfBins bug
#8
alexandruioanvoda
closed
5 years ago
1
Missing parameter error
#7
alexandruioanvoda
closed
5 years ago
2
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