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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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unitig size
#169
annarerra
closed
2 years ago
3
recombination rate adjustment
#168
annarerra
closed
2 years ago
6
annotation of SNPs as for kmers
#167
annarerra
closed
2 years ago
2
no significant genes using --vcf mode
#166
annarerra
closed
2 years ago
2
Enet/lasso fails with "ValueError: negative dimensions are not allowed"
#165
mgalardini
opened
2 years ago
2
Do not crash when saving wg model w/ covariates
#164
mgalardini
closed
2 years ago
0
Print the lineage header with whole genome
#163
mgalardini
closed
2 years ago
0
WG mode should print out the lineage column header for selected variants
#162
mgalardini
closed
2 years ago
0
Fix elastic net with lineages
#161
johnlees
closed
3 years ago
2
UnboundLocalError: local variable 'lineage_clusters_full' referenced before assignment
#160
jpaganini
closed
3 years ago
5
Dealing with intra-patient diversity -- covariates with elastic net model?
#159
cizydorczyk
closed
2 years ago
5
ignores missing entries in .Rtab files
#158
julibeg
opened
3 years ago
8
missing data is ignored with variant files but not .Rtab
#157
julibeg
opened
3 years ago
4
Interpretation of the results of Wald test for association between lineages and phenotype
#156
neginmb
opened
3 years ago
3
AttributeError: 'list' object has no attribute 'kmer'
#155
francesccoll
closed
3 years ago
2
perform Firth regression when hitting matrix-inversion-error
#154
julibeg
closed
3 years ago
1
ValueError when input has variants that don't occur in a single sample
#153
julibeg
opened
3 years ago
2
Add shape parameter to csr_matrix in load_all_vars (#151)
#152
julibeg
closed
3 years ago
3
load_all_vars throws IndexError
#151
julibeg
closed
3 years ago
6
Abort when --lmm but no similarity/cache provided
#150
mgalardini
closed
3 years ago
0
Format of lineage.txt
#149
buihoangphuc412
closed
3 years ago
2
Version bump
#148
mgalardini
closed
3 years ago
4
Change the way pre-filtered variants are reported
#147
mgalardini
closed
3 years ago
1
Filtering based on maximum allele frequency
#146
neginmb
closed
3 years ago
18
IndexError-list index out of range
#145
buihoangphuc412
closed
3 years ago
10
False positive results caused by multicopy sequences such as rRNA or Transposase
#144
Daikuang
closed
3 years ago
4
IndexError: list index out of range when using unitig-caller output
#143
jolindadekorne
closed
3 years ago
3
Remove second midroot now dendropy is fixed
#142
johnlees
closed
3 years ago
0
AssertionError in dendropy when running scripts/phylogeny_distance.py
#141
julibeg
closed
3 years ago
1
Add test that phenotype is numeric
#140
johnlees
closed
3 years ago
4
TypeError: unsupported operand type(s) for /: 'str' and 'int'
#139
Morteza-M-Saber
closed
3 years ago
2
Significant hits when measured heritability is zero
#138
Morteza-M-Saber
closed
3 years ago
1
`LinAlgError: Singular matrix` in fitting SEER model only occurs with LRR as intercept in `start_vec`
#137
julibeg
closed
3 years ago
6
Do you apply any transformation for the continuous trait in case it does not follow a normal distribution?
#136
neginmb
opened
3 years ago
9
problem with analysis of COGs
#135
pavlo888
closed
3 years ago
6
Trying to run tutorial and getting an eror
#134
waalkes
closed
3 years ago
13
No gene name in unitig annotation
#133
samlipworth
closed
3 years ago
5
Problem with k-mer association
#132
mi3112
closed
3 years ago
3
Docs: covariates want a header
#131
mgalardini
closed
3 years ago
0
Covariate file expects header
#130
apredeus
closed
3 years ago
1
Inflated QQ plot
#129
apredeus
closed
3 years ago
5
ValueError: zero-size array to reduction operation maximum which has no identity
#128
reedus-123
closed
3 years ago
10
Question: how to identify which phenotype a variant/kmer is associated with?
#127
reedus-123
closed
3 years ago
11
Fix summarize_annotations when using elastic net
#126
lvclark
closed
3 years ago
8
bad-chisq
#125
zmy24
closed
3 years ago
2
phylogeny_distance.py result not symmetric
#124
RicardoGCCR
closed
3 years ago
4
Error running example
#123
vealvarez
closed
3 years ago
2
MemoryError when using --lineage-clusters and --sequence-reweighting
#122
boasvdp
closed
3 years ago
2
Can't install with conda on Windows due to "incompatibility" with 0 other packages
#121
dkassler
closed
4 years ago
1
--max-missing in pyseer is not working.
#120
neginmb
closed
4 years ago
7
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