mgalardini/pyseer

Issues

• Annotating unitigs using annotate_hits_pyseer

  #272 opened 5 months ago by daisy238
  8

• Number of significant genes different with several runs of Pyseer

  #264 opened 10 months ago by Samriddhi0906
  6

• manhattan plot

  #273 opened 5 months ago by xqzangnolan
  0

• vcf GT format:0/0, 1/1 or 0 , 1

  #241 opened 5 months ago by yayahoho1
  4

• Suggestions needed for the whole-genome model output

  #243 opened 5 months ago by AmayAgrawal
  2

• fsm-lite stops due to lack of RAM

  #259 opened 5 months ago by hfaoro
  3

• Seeking combined effects of variants on a continuous phenotype with pyseer elastic nets

  #261 opened 5 months ago by vijuvi
  10

• Getting Intergenic regions, sRNAs and ORF from pyseer

  #262 opened 5 months ago by AbubakariAbdulwasid
  4

• merged snps files

  #266 opened 5 months ago by akarkaba
  2

• Prediction Tutorial Error

  #267 opened 5 months ago by chaseschwarz
  2

• k-mer annotation

  #270 opened 5 months ago by beryl-au
  6

• SNP and COG association with fixed effects model

  #271 opened 5 months ago by OtakuZerg
  4

• K-mer association with mixed effects model

  #265 opened 8 months ago by komaltilwani53
  6

• "UnsatisfiableError" when trying to install pyseer with conda

  #263 opened 10 months ago by dennisdharmawan
  2

• Possible problem with VCF file meaning 0 tested/printed variants

  #260 opened a year ago by michhulin
  2

• rsync webhook for docs

  #258 opened a year ago by johnlees
  0

• SNPs GWAS

  #257 opened a year ago by AbubakariAbdulwasid
  6

• Update readthedocs config

  #248 opened a year ago by johnlees
  1

• Annotating Kmers in RNA regions

  #253 opened a year ago by idolawoye
  4

• Fatal glmnet error when trying to fit an elastic net model on training set

  #252 opened a year ago by vijuvi
  14

• Change the CI from conda to mamba

  #247 opened a year ago by johnlees
  1

• No tested/printed variants

  #251 opened a year ago by idolawoye
  1

• many lrt-filtering-failed with very low filter-pvalues

  #249 opened a year ago by waalkes
  8

• burden testing, gene length

  #250 opened a year ago by dustinlong
  2

• ZeroDivisionError (0variants [00:00, ?variants/s])

  #245 opened a year ago by GaloGS
  4

• Abricate compatibility issue

  #244 opened a year ago by chunmn826
  3

• Regarding adjusting for population structure when detecting lineage-specific sequence

  #242 opened 2 years ago by snackens
  1

• annotation criteria when matching reference

  #240 opened 2 years ago by snackens
  4

• lineage specific unitigs

  #238 opened 2 years ago by snackens
  10

• ValueError: could not convert string to float error in mash dist mash_sketch.msh mash_sketch.msh| square_mash > mash.tsv

  #215 opened 2 years ago by Albertzhuo123
  7

• Using unitigs generated from short-reads

  #223 opened 2 years ago by WMonteith
  2

• Multiple annotations per kmer, prevents summarization

  #228 opened 2 years ago by jacordova
  6

• Problem installing pyseer with conda

  #232 opened 2 years ago by ireneortega
  4

• Fixed or mixed effects model?

  #234 opened 2 years ago by ireneortega
  2

• snp.vcf file

  #233 opened 2 years ago by hfaoro
  3

• Getting error while installing pyseer using miniconda

  #225 opened 2 years ago by dzjian2
  1

• possibly erroneous odds ratio?

  #227 opened 2 years ago by alexlevylab
  3

• Do the tree for calculating the kinship matrix should be rooted?

  #226 opened 2 years ago by Tonny-zhou
  1

• VCF input requires bgzip and tabix index

  #229 opened 2 years ago by LeahRoberts
  1

• Multiple alleles similarity_pyseer

  #231 opened 2 years ago by ireneortega
  1

• glmnet version pip install

  #230 opened 2 years ago by LeahRoberts
  1

• QQ plot graphs

  #222 opened 2 years ago by AlperYurtseven
  1

• GWAS analysis using both SNP and COG together

  #224 opened 2 years ago by AmayAgrawal
  1

• Evaluate the results

  #221 opened 2 years ago by AlperYurtseven
  2

• similarity_pyseer generates a matrix with all 0's

  #220 opened 2 years ago by AmayAgrawal
  5

• pyseer Manhattan plot can´t be seen in Phandango

  #218 opened 2 years ago by rachel1898
  4

• Adding multidimensionality to cmdscale

  #217 opened 2 years ago by BernardoOlisan
  1

• Improve error messages when wrong format is used

  #216 opened 2 years ago by mgalardini
  0

• qq plot

  #212 opened 2 years ago by ShiminYang97
  7

• Error in annotate_hits_pyseer

  #208 opened 3 years ago by nicola-palmieri
  3