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Bump numpy from 1.18.1 to 1.22.0
#37
dependabot[bot]
opened
2 years ago
0
Bump ipython from 7.12.0 to 7.16.3
#36
dependabot[bot]
opened
2 years ago
0
Bump pygments from 2.5.2 to 2.7.4
#35
dependabot[bot]
opened
3 years ago
0
A few minor fixes
#34
James-S-Santangelo
closed
4 years ago
1
Adding Argparse, parameters, and general cleanup
#33
James-S-Santangelo
closed
4 years ago
1
Update vcf2fasta script and add documentation
#32
aays
closed
4 years ago
0
Try using E(r2) eqn from Hill and Weir 1988 to fit for genome-wide recombination rate
#31
aays
opened
4 years ago
1
Switch to using Drosophila
#30
aays
closed
4 years ago
7
Run ldhelmet on server
#29
James-S-Santangelo
closed
4 years ago
0
Small changes to batch scripts on server
#28
James-S-Santangelo
closed
4 years ago
0
Adding sequence length functionality
#27
James-S-Santangelo
closed
4 years ago
1
Vary sequence length in simulations and VCF2fasta conversion
#26
James-S-Santangelo
closed
4 years ago
0
Changes to batch script to run on server
#25
James-S-Santangelo
closed
4 years ago
1
Some cleanup
#24
aays
closed
4 years ago
1
Remove annotation table dependence in VCF to FASTA script
#23
aays
closed
4 years ago
1
Parallelize VCF to FASTA operation using multiprocessing module
#22
aays
opened
4 years ago
0
Convert VCF to Fasta
#21
James-S-Santangelo
closed
4 years ago
1
Use LDJump to analyse recombination rate
#20
James-S-Santangelo
opened
4 years ago
1
Refactor ANT.py script
#19
James-S-Santangelo
closed
4 years ago
0
Add Rproject and packrat to repo for R analyses
#18
James-S-Santangelo
closed
4 years ago
0
Sort and Tabix index VCFs
#17
James-S-Santangelo
closed
4 years ago
1
Convert VCFs to Fasta
#16
James-S-Santangelo
closed
4 years ago
0
Sort VCFs and convert to LDhat format
#15
James-S-Santangelo
closed
4 years ago
1
Changing output paths and bgzipping
#14
James-S-Santangelo
closed
4 years ago
1
Separate output folders for different parameter combinations
#13
James-S-Santangelo
closed
4 years ago
0
Added random seed to slim simulations
#12
James-S-Santangelo
closed
4 years ago
0
Bgzip
#11
James-S-Santangelo
closed
4 years ago
1
Add random seed for SLiM sims
#10
James-S-Santangelo
closed
4 years ago
0
Separate function for arguments passed to Argparse
#9
James-S-Santangelo
closed
4 years ago
0
Parse LDhat output to obtain rho
#8
James-S-Santangelo
closed
4 years ago
1
Parallel processing of simulations by LDhat
#7
James-S-Santangelo
closed
4 years ago
1
Parallel conversion of VCFs to LDhat format
#6
James-S-Santangelo
closed
4 years ago
1
Add functionality to bgzip vcfs
#5
James-S-Santangelo
closed
4 years ago
0
Script cleanup
#4
James-S-Santangelo
closed
4 years ago
2
Add optional arguments to vary mutation rate and recombination rate
#3
James-S-Santangelo
closed
4 years ago
0
Server organisation and next steps
#2
James-S-Santangelo
closed
4 years ago
1
Initial repo cleanup
#1
James-S-Santangelo
closed
4 years ago
1