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dvitale199
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GenoTools
GenoTools: Advanced Genotype Data Analysis A robust suite for processing genotype data, offering genotype calling (.idat to PLINK), comprehensive sample/variant QC, and ancestry estimation. Ideal for computational biology and genetics research.
Apache License 2.0
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Update documentation
#189
nvk23
closed
1 week ago
0
het typo
#188
sammyhong23
closed
1 week ago
0
Update qc.py
#187
dvitale199
closed
1 month ago
0
check for abspath for concat_logs for relative path execution
#186
dvitale199
closed
1 month ago
0
updated het to +/-0.15
#185
dvitale199
closed
2 months ago
0
Related
#184
dvitale199
closed
2 months ago
0
removed snp filtering from kinship in run_related_prune()
#183
dvitale199
closed
2 months ago
0
Update cli_args.md
#182
dvitale199
closed
2 months ago
0
Update README.md
#181
dvitale199
closed
3 months ago
0
Problem with temporary files
#180
gdejana
closed
3 months ago
4
separate ancestry from execute_pipeline
#179
mkoretsky1
closed
4 months ago
0
min sample error catching for --ld
#178
dvitale199
opened
4 months ago
1
Update README.md
#177
dvitale199
closed
4 months ago
0
model training and ref panel prep docs
#176
mkoretsky1
closed
4 months ago
0
Update json_output_overview.md
#175
dvitale199
closed
5 months ago
0
Test hap
#174
mkoretsky1
closed
5 months ago
0
update warning for covar/pca
#173
sammyhong23
closed
5 months ago
0
Adjust gwas module to allow for any phenotype (not just PHENO1)
#172
dvitale199
opened
5 months ago
0
reading pvar to skip # columns and explicitely stating names in genot…
#171
dvitale199
closed
5 months ago
0
get case/control counts by value not by index
#170
mkoretsky1
closed
5 months ago
0
Failure to read pvar in upfront_check if it came from a vcf with header rows '##'
#169
dvitale199
closed
5 months ago
0
Update README.md
#168
dvitale199
closed
5 months ago
0
King dependency
#167
sammyhong23
closed
5 months ago
0
Kinship check
#166
sammyhong23
closed
6 months ago
0
Dependencies
#165
dvitale199
closed
6 months ago
0
load json component example
#164
mkoretsky1
closed
6 months ago
0
update json for --visualize and create docs
#163
mkoretsky1
closed
6 months ago
0
KeyError: 'FID' when merging for labeled_pruned_df
#162
zihhuafang
closed
5 months ago
0
Update dependencies.py
#161
dvitale199
closed
6 months ago
0
Run gwas linear
#160
mikayla-james
closed
6 months ago
0
adjust haplo prune pval based on sample size
#159
mkoretsky1
closed
7 months ago
0
added static method for inflation
#158
dvitale199
closed
7 months ago
0
.linear not captured in run_gwas() for linear phenotypes
#157
dvitale199
closed
4 months ago
0
insufficient ancestry count to pruned samples json output
#156
mkoretsky1
closed
7 months ago
0
ancestry in pruned samples table
#155
mkoretsky1
closed
7 months ago
0
remove duplicated ancestry labels df in json output
#154
mkoretsky1
closed
7 months ago
0
combine covars with PCs if --covars and --pca called
#153
dvitale199
opened
7 months ago
0
test acc in json
#152
mkoretsky1
closed
8 months ago
0
Update CITATION.cff
#151
dvitale199
closed
8 months ago
0
min samples flag and copy related files to out_path
#150
mkoretsky1
closed
8 months ago
0
Update CITATION.cff Kristin
#149
mkoretsky1
closed
8 months ago
0
Update CITATION.cff
#148
sammyhong23
closed
8 months ago
0
Update CITATION.cff Koretsky
#147
mkoretsky1
closed
8 months ago
0
Update README.md
#146
dvitale199
closed
8 months ago
0
updated warnings to stacklevel=2
#145
dvitale199
closed
8 months ago
0
if statements to check if outputs from hap and hwe variant pruning cr…
#144
dvitale199
closed
8 months ago
0
adding mis_rm_counts for case_control fail
#143
mkoretsky1
closed
8 months ago
0
switching --warn default
#142
mkoretsky1
closed
8 months ago
0
containerized predictions fail due to permissions in the container
#141
dvitale199
opened
8 months ago
0
removed plotting from ancestry.py
#140
dvitale199
closed
8 months ago
0
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