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mgalardini
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pyseer
SEER, reimplemented in python 🐍🔮
http://pyseer.readthedocs.io
Apache License 2.0
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Enet covariates
#219
mgalardini
closed
1 year ago
1
pyseer Manhattan plot can´t be seen in Phandango
#218
rachel1898
closed
1 year ago
4
Adding multidimensionality to cmdscale
#217
BernardoOlisan
closed
1 year ago
1
Improve error messages when wrong format is used
#216
mgalardini
opened
1 year ago
0
ValueError: could not convert string to float error in mash dist mash_sketch.msh mash_sketch.msh| square_mash > mash.tsv
#215
Albertzhuo123
closed
1 year ago
7
Version bump
#214
mgalardini
closed
1 year ago
0
Fix QQ-plot
#213
mgalardini
closed
1 year ago
0
qq plot
#212
ShiminYang97
closed
1 year ago
7
Make the similarity script work
#211
mgalardini
closed
1 year ago
0
Update docs on effect sizes
#210
johnlees
closed
2 years ago
0
Sanitize full path inputs for gff2bed
#209
mgalardini
closed
2 years ago
0
Error in annotate_hits_pyseer
#208
nicola-palmieri
closed
2 years ago
3
pyseer running issue
#207
sekhwal
closed
2 years ago
10
Add a script to compute a covariance matrix from unitigs presence/absence
#206
mgalardini
closed
2 years ago
2
DO not run WG with --output-patterns
#205
mgalardini
closed
2 years ago
0
How to run pyseer with vcf files
#204
sekhwal
closed
2 years ago
6
Empty kmer_patterns.txt file with --wg enet
#203
charlottecc
closed
2 years ago
8
Population structure not being corrected sufficiently
#202
smb20200615
closed
2 years ago
1
Confidence intervals for beta
#201
samlipworth
closed
2 years ago
2
few kmer hits in unitig GWAS
#200
smb20200615
closed
2 years ago
4
Remove requirements from docs setup.py
#199
johnlees
closed
2 years ago
0
Bad ChiSq Only for isolates
#198
noahaus
closed
2 years ago
1
deflated values
#197
mac137
closed
2 years ago
4
Using phylogeny based distance vs mash distance for lineage effects
#196
ss8222
closed
2 years ago
1
Question about lineage/loci association
#195
smb20200615
closed
2 years ago
12
Doc build failing
#194
johnlees
closed
2 years ago
0
Explicit kwargs for sklearn
#193
mgalardini
closed
2 years ago
0
How to deal with linkage in the data
#192
martinastoycheva
closed
2 years ago
3
pytest :test_load_structure fails
#191
linaule
closed
2 years ago
1
solved
#190
xuefenfei712
closed
2 years ago
0
Perfectly separable data error for null model
#189
nicola-palmieri
closed
2 years ago
2
Population structure based on phylogeny - rooting of tree
#188
Vers4L
closed
2 years ago
1
Calculating LD post annotating significant unitig/kmer
#187
Srividhya-Sainath
closed
2 years ago
2
Don't know how to start analysis
#186
GillNdhlovu
closed
2 years ago
1
mapping snps
#185
annarerra
closed
2 years ago
8
Mapping kmers to single reference genome
#184
Srividhya-Sainath
closed
2 years ago
1
Mapping hits using a pangenome
#183
LeonardosMageiros
opened
2 years ago
4
Error while pip3 installing pyseer
#182
Srividhya-Sainath
closed
2 years ago
2
More than two phenotypes (not-continuous) and multiple hypotheses correction
#181
VadimDu
closed
2 years ago
1
Lineage-associated mutations
#180
sydelstan
opened
2 years ago
10
Using unitigs to predict with elastic net
#179
LeonardosMageiros
closed
2 years ago
1
COG pvalue threshold and qq plot
#178
LeonardosMageiros
closed
2 years ago
6
Direction of association in the summarised results
#177
LeonardosMageiros
closed
2 years ago
4
Generating manhattan plot
#176
smb20200615
closed
2 years ago
2
phandango manhattan plot
#175
annarerra
closed
2 years ago
2
SNP vs K-mer
#174
neginmb
opened
2 years ago
1
lmm lineage effects + unique variant patterns
#173
sydelstan
closed
2 years ago
1
Gene description in the significant hits summary
#172
LeonardosMageiros
opened
2 years ago
0
summarised results questions
#171
LeonardosMageiros
closed
2 years ago
3
gene annotation
#170
annarerra
closed
2 years ago
2
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