molgenis/systemsgenetics

Issues

• Error during GADO prioritisation when it encounters an unexpected HPO term

  #671 opened 3 months ago by souzadevinicius
  3

• how to extract the expression numerical matrix of SNPS?

  #672 opened a month ago by ChaoXianSen
  3

• gene_network_decomposition.py

  #669 opened 5 months ago by biopig
  1

• How to select significant cell type eQTL

  #668 opened 9 months ago by zhangpicb
  6

• [Genotype Harmonizer] Bug Report: Confusing Problems on SNPs excluding

  #667 opened 9 months ago by jacklin9703
  0

• Not all variants are flipped

  #666 opened 10 months ago by abedkurdi
  0

• can't open eQTLGen now

  #665 opened a year ago by LynnChan99
  0

• [Genotype-IO] Error parsing VCF info column value

  #664 opened a year ago by Bonder-MJ
  0

• GADO doesn't produce `all_samples.txt` in some cases

  #663 opened a year ago by dennishendriksen
  0

• Can't download jar for eQTL analyzer

  #660 opened a year ago by BennyStrobes
  6

• Decon-eQTL

  #642 opened 2 years ago by TatiKarp
  2

• difficults in using Genotype Harmonizer

  #637 opened 2 years ago by malu-rdz
  1

• Error when converting .vcf file to .bgen: "Phased data not available"

  #632 opened 2 years ago by DanKaptijn
  2

• GADO command line issue, gene prioritization doesn't work

  #628 opened 2 years ago by zhouyunyun11
  0

• tabix support for CSI index

  #619 opened 2 years ago by ClayBirkett
  1

• Increase the usage of compound assignment operators

  #605 opened 3 years ago by elfring
  0

• Downstreamer : java.lang.RuntimeException: java.lang.ArrayIndexOutOfBoundsException

  #604 opened 3 years ago by nrosewick
  3

• Dependencies issues Downstreamer

  #603 opened 3 years ago by nrosewick
  0

• Chromosome X

  #601 opened 3 years ago by DanielEWeeks
  1

• GADO profiles update

  #586 opened 4 years ago by edg1983
  7

• can not open this list

  #598 opened 3 years ago by lizhebio
  0

• Decon-eQTL dosage and snpsToTest

  #595 opened 3 years ago by cindywen96
  3

• Decon-eQTL - dosage file missing values

  #589 opened 4 years ago by mooreann
  1

• Strand alignment error

  #587 opened 4 years ago by ConnieXuhm
  1

• Decon-eQTL: Expression file needing snp?

  #579 opened 4 years ago by mooreann
  1

• decon-eQTL genotype file

  #577 opened 4 years ago by mooreann
  1

• INFO - Variants where not sorted, loading will be faster if the data is pre-sorted

  #578 opened 4 years ago by onebeingmay
  1

• Eosinophils

  #554 opened 4 years ago by antgomo
  1

• Multipart genotype files

  #568 opened 4 years ago by Bonder-MJ
  0

• VCF Probability fall back from phased to unphased

  #569 opened 4 years ago by Bonder-MJ
  0

• Clarifying the license?

  #562 opened 4 years ago by tomsing1
  1

• Error on Example Run

  #518 opened 6 years ago by ONeillMB1
  3

• Error when running pcaoptimum - also applies to mixupmapper

  #515 opened 6 years ago by ds763
  0

• "Error writing output data:Trying to write alleles" Issue?

  #492 opened 6 years ago by wwhengold
  3

• Is it possible to get the output of GenotypeHarmonizer as VCF ?

  #491 opened 6 years ago by drveera
  1

• Alignment of monomorphic SNPs (plink format) by Genotype harmonizer

  #482 opened 7 years ago by zhengxuhao
  3

• Genotype Harmonizer --hweFilter minimum p-value?

  #489 opened 7 years ago by juliedwhite
  2

• Writing on multi allelic SNPs

  #485 opened 7 years ago by Bonder-MJ
  0

• Missing values ImputedDosageMatrix.dat

  #481 opened 7 years ago by harmbrugge
  0

• Output to Bed Issues

  #480 opened 7 years ago by albeele1
  2

• Genotype Harmonizer an option to drop A/T C/G altogether

  #475 opened 7 years ago by gaow
  2

• Fix Genotype-IO/pom.xml dependency issues

  #479 opened 7 years ago by dennishendriksen
  0

• Link to PLINK website in eQTL manual is broken

  #474 opened 7 years ago by npklein
  3

• GenotypeHarmonizer installation issue?

  #473 opened 7 years ago by anderseng
  1

• Possible error in how the ASEperRegion module tracks the dispersion estimates

  #468 opened 8 years ago by arunkom
  6

• input file request for genotype harmonizer

  #467 opened 8 years ago by sarahcn
  1

• cellTypeSpecificAlleleSpecificExpression: filename and sample names

  #454 opened 8 years ago by colindaven
  16

• Coverage reporting no longer works

  #445 opened 8 years ago by fdlk
  0

• Subproject versions have diverged

  #447 opened 8 years ago by fdlk
  3

• Link to JAR dead

  #443 opened 8 years ago by colindaven
  2