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bodkan
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admixr
An R package for reproducible and automated ADMIXTOOLS analyses
https://bodkan.net/admixr
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Fast printing of EIGENSTRAT objects
#41
bodkan
closed
5 years ago
1
Fix parsing errors for duplicated populations
#40
bodkan
closed
5 years ago
0
Remove C++ dependencies
#39
bodkan
closed
5 years ago
0
C++ implementation of VCF -> EIGENSTRAT conversion
#38
bodkan
closed
5 years ago
0
Full implementation of qpWave and qpAdm
#37
bodkan
closed
5 years ago
0
Change SNP counting, EIGENSTRAT construction and printing
#36
bodkan
closed
5 years ago
0
Check log file before parsing in case ADMIXTOOLS crashes
#35
bodkan
closed
5 years ago
2
Add a faster VCF --> EIGENSTRAT parser
#34
bodkan
closed
5 years ago
1
Add description of adding ADMIXTOOLS to $PATH
#33
bodkan
closed
4 years ago
0
Add possibility to calculate f3 for all combinations
#32
bodkan
closed
4 years ago
0
Specify new population labels directly, not via list
#31
bodkan
closed
6 years ago
0
Re-write the package to make it more %>% friendly
#30
bodkan
closed
6 years ago
0
Find a way to specify the paths to ADMIXTOOLS binaries
#29
bodkan
closed
4 years ago
1
Figure out a way to automatically build package website during Travis CI builds
#28
bodkan
closed
5 years ago
0
Add R wrapper around `mergeit`
#27
bodkan
closed
6 years ago
1
Organize exported functions in the reference list
#26
bodkan
closed
6 years ago
0
Make subset_sites function more generic
#25
bodkan
closed
6 years ago
1
Make sure that temporary files are properly cleaned up
#24
bodkan
closed
6 years ago
1
Use `use_pipe`?
#23
bodkan
closed
6 years ago
0
Make function names more readable
#22
bodkan
closed
6 years ago
0
Implement better file path handling
#21
bodkan
closed
6 years ago
0
Deal with the "best" entry in a D statistics output
#20
bodkan
closed
6 years ago
1
Check for ADMIXTOOLS presence
#19
bodkan
closed
6 years ago
0
Can we use "SSS" and "DIR" options?
#18
bodkan
closed
6 years ago
0
Install ADMIXTOOLS into a Travis CI environment for future testing
#17
bodkan
closed
6 years ago
1
Add an option to save ADMIXTOOLS config/par files with sensible names
#16
bodkan
closed
6 years ago
2
Let qpDstat calculate the standard errors
#15
bodkan
closed
6 years ago
1
Use data.table instead of dplyr
#14
bodkan
closed
6 years ago
1
Prevent unnecessary warning/message info in read_geno/read_ind/read_snp
#13
bodkan
closed
6 years ago
1
Add a vignette describing "the old way" vs "the new way" for running ADMIXTOOLS analysis
#12
bodkan
closed
6 years ago
0
Add a tiny utility function for loading and writing EIGENSTRAT data in data.frames
#11
bodkan
closed
6 years ago
1
Export VCF from EIGENSTRAT
#10
bodkan
closed
6 years ago
1
Fix issues with functions from external libraries not being available
#9
bodkan
closed
7 years ago
1
Add support for the "poplistname" option in qpDstat
#8
bodkan
closed
6 years ago
1
Check for a presence of individuals in an "ind" file
#7
bodkan
closed
7 years ago
0
Import from VCF into EIGENSTRAT
#6
bodkan
closed
6 years ago
3
Convert ADMIXTOOLS warnings to R warnings
#5
bodkan
closed
5 years ago
2
Convenient function for generating badsnp_file
#4
bodkan
closed
6 years ago
1
A single function to read all output
#3
bodkan
closed
6 years ago
0
Add a proper README
#2
bodkan
closed
6 years ago
0
Add tests for the wrapper functionality
#1
bodkan
closed
6 years ago
0
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