mgalardini pyseer issues

mgalardini / pyseer

SEER, reimplemented in python 🐍🔮

http://pyseer.readthedocs.io

Apache License 2.0

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issues

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Avoid unit test failures with newer sklearn

#269 mgalardini closed 4 days ago
1
added option to print computed p-value threshold

#268 Bamu-d closed 1 week ago
1
Prediction Tutorial Error

#267 chaseschwarz opened 3 weeks ago
1
merged snps files

#266 akarkaba opened 1 month ago
1
K-mer association with mixed effects model

#265 komaltilwani53 opened 1 month ago
6
Number of significant genes different with several runs of Pyseer

#264 Samriddhi0906 opened 4 months ago
2
"UnsatisfiableError" when trying to install pyseer with conda

#263 dennisdharmawan closed 4 months ago
2
Getting Intergenic regions, sRNAs and ORF from pyseer

#262 AbubakariAbdulwasid opened 5 months ago
3
Seeking combined effects of variants on a continuous phenotype with pyseer elastic nets

#261 vijuvi opened 5 months ago
9
Possible problem with VCF file meaning 0 tested/printed variants

#260 michhulin closed 5 months ago
2
fsm-lite stops due to lack of RAM

#259 hfaoro opened 7 months ago
2
rsync webhook for docs

#258 johnlees opened 7 months ago
0
SNPs GWAS

#257 AbubakariAbdulwasid closed 7 months ago
6
Docs: fix readthedocs build failure

#256 mgalardini closed 7 months ago
1
CI: use mamba

#255 mgalardini closed 7 months ago
0
Add option to allow intersection with other feature types other than CDSs

#254 mgalardini closed 7 months ago
0
Annotating Kmers in RNA regions

#253 idolawoye closed 7 months ago
4
Fatal glmnet error when trying to fit an elastic net model on training set

#252 vijuvi closed 7 months ago
14
No tested/printed variants

#251 idolawoye closed 8 months ago
1
burden testing, gene length

#250 dustinlong closed 8 months ago
2
many lrt-filtering-failed with very low filter-pvalues

#249 waalkes closed 8 months ago
8
Update readthedocs config

#248 johnlees closed 7 months ago
1
Change the CI from conda to mamba

#247 johnlees closed 7 months ago
1
Refuse to run in a certain configuration in fixed effects mode

#246 mgalardini closed 9 months ago
0
ZeroDivisionError (0variants [00:00, ?variants/s])

#245 GaloGS closed 9 months ago
4
Abricate compatibility issue

#244 chunmn826 closed 9 months ago
3
Suggestions needed for the whole-genome model output

#243 AmayAgrawal opened 11 months ago
1
Regarding adjusting for population structure when detecting lineage-specific sequence

#242 snackens closed 1 year ago
1
vcf GT format:0/0, 1/1 or 0 , 1

#241 yayahoho1 opened 1 year ago
1
annotation criteria when matching reference

#240 snackens closed 1 year ago
4
Properly formatted output table w/o distances

#239 mgalardini closed 1 year ago
2
lineage specific unitigs

#238 snackens closed 1 year ago
10
Rtab files can encode missing values with an empty string

#237 mgalardini closed 1 year ago
0
Consider that a distance matrix may not be symmetrical

#236 mgalardini closed 1 year ago
0
More robust annotation parsing

#235 johnlees closed 1 year ago
1
Fixed or mixed effects model?

#234 ireneortega closed 1 year ago
2
snp.vcf file

#233 hfaoro closed 1 year ago
3
Problem installing pyseer with conda

#232 ireneortega closed 1 year ago
4
Multiple alleles similarity_pyseer

#231 ireneortega closed 1 year ago
1
glmnet version pip install

#230 LeahRoberts closed 1 year ago
1
VCF input requires bgzip and tabix index

#229 LeahRoberts closed 1 year ago
1
Multiple annotations per kmer, prevents summarization

#228 jacordova closed 1 year ago
6
possibly erroneous odds ratio?

#227 alexlevylab closed 1 year ago
3
Do the tree for calculating the kinship matrix should be rooted?

#226 Tonny-zhou closed 1 year ago
1
Getting error while installing pyseer using miniconda

#225 dzjian2 closed 1 year ago
1
GWAS analysis using both SNP and COG together

#224 AmayAgrawal closed 1 year ago
1
Using unitigs generated from short-reads

#223 WMonteith closed 1 year ago
2
QQ plot graphs

#222 AlperYurtseven closed 1 year ago
1
Evaluate the results

#221 AlperYurtseven closed 1 year ago
2
similarity_pyseer generates a matrix with all 0's

#220 AmayAgrawal closed 1 year ago
5