YuLab-SMU/DOSE

Issues

• `Error in get("DOLite2EG") : object 'DOLite2EG' not found` when re-run `enrichDO`

  #85 opened 4 months ago by zxy0912
  1

• GSEA to discover mixed enriched terms

  #84 opened 8 months ago by mauritsunkel
  1

• EXTID2NAME fails to convert geneID to symbol in org.Sc.sgd.db

  #83 opened a year ago by janedut
  1

• Error in findPathClusters(enrich, cluster = "hier", minClusterSize = 3) : could not find function "findPathClusters"

  #81 opened a year ago by MANZHAOHUI
  1

• MPO.db/HPO.db installation error

  #79 opened a year ago by ushione
  3

• MPO.db installation error

  #78 opened a year ago by eudoraleer
  6

• Parameter "universe" is not properly handled in "enricher" function

  #74 opened a year ago by soumitrakp
  3

• Some problems about 'maxGSSize' parameter in enricher_interval series function

  #28 opened 5 years ago by huangwb8
  1

• Seed used in GSEA_fgsea is (almost always) the same

  #76 opened a year ago by vgilbart
  0

• Query regarding probability computation in enricher_internal function

  #73 opened 2 years ago by soumitrakp
  1

• cnetplot for selected gene and GO term

  #70 opened 2 years ago by antoine4ucsd
  1

• drimseq-error

  #72 opened 2 years ago by pragathi-sneha
  0

• Error installing latest version of DOSE

  #69 opened 2 years ago by archanabhardwaj
  1

• How to add only needed enriched terms in dotplot or cnetplot

  #64 opened 3 years ago by pragathi-sneha
  1

• Universal background gene list used in enricher function

  #62 opened 3 years ago by merckey
  1

• visualizing GSEA results with 'dotplot'

  #20 opened 3 years ago by guidohooiveld
  35

• Rationale for decreasing order only in GSEA

  #58 opened 3 years ago by Nelson-Gon
  4

• [Feature Request] Allow conversion to columns other than hgnc symbol

  #63 opened 3 years ago by Nelson-Gon
  0

• DO.db过于老旧

  #57 opened 3 years ago by GuangchuangYu
  2

• reproducibility of GSEA

  #4 opened 3 years ago by vladpetyuk
  1

• How does showCategory function work?

  #54 opened 3 years ago by smk5g5
  2

• setReadable not returning correct gene symbol

  #41 opened 3 years ago by alexyfyf
  4

• own genelist; too dump top proceed

  #55 opened 3 years ago by mocherry
  3

• Issues w/expected input genes

  #35 opened 4 years ago by jinkinson
  3

• Saving separate dotplots with for loop

  #48 opened 4 years ago by mirkocelii
  1

• enricher_internal.R code may have mistake

  #52 opened 3 years ago by tangmaomao16
  1

• setReadable for compareCluster output

  #43 opened 3 years ago by GuangchuangYu
  1

• No genes mapped by gseNCG

  #47 opened 4 years ago by gabrieljmarques
  0

• bug in DOSE:::gseaScores - Error in if (abs(max.ES) > abs(min.ES))

  #46 opened 4 years ago by therealgenna
  9

• gseGO through fgsea [ by GSEA_internal() ] is not fully reproducible, but is when running fgsea directly

  #45 opened 4 years ago by guidohooiveld
  2

• Can I make similar ontology package using DOSE？

  #38 opened 4 years ago by shangguandong1996
  4

• enrichNCG - update the database

  #33 opened 4 years ago by ABanaeiEsfahani
  2

• Error: object 'upsetplot' not found

  #31 opened 5 years ago by TimJCooper
  1

• information content calculation discordance

  #27 opened 6 years ago by ieiwk
  0

• Disrepancy GSEA results when using by="DOSE" or by="fgsea"

  #18 opened 8 years ago by guidohooiveld
  3

• P-value cutoff _also_ applied to adjusted P-value

  #26 opened 6 years ago by kevinrue
  0

• segfault while installing

  #25 opened 7 years ago by gaiazaff
  9

• DOSE::gseaplot v3.4.0 does NOT plot Running Enrichment Score correctly

  #23 opened 7 years ago by Ni-Ar
  8

• GSEA result p.adjust vs qvalue

  #24 opened 7 years ago by mgandal
  0

• Update to DisGeNet 5?

  #22 opened 7 years ago by tonigi
  2

• Some functions documented are not exported

  #21 opened 8 years ago by llrs
  3

• Question: How to combine multiple enrichmentResult objects

  #12 opened 8 years ago by wyu
  5

• compareCluster error

  #19 opened 8 years ago by Georgewiggins
  1

• gseDO() example doesn't run

  #16 opened 8 years ago by guidohooiveld
  10

• Unable to plot with enrichMap

  #15 opened 8 years ago by llrs
  7

• enrichGO() gives incorrect results due to different filtering of gene and universe set

  #11 opened 8 years ago by Gig77
  7

• GSEA() qvalue error when using very few terms

  #10 opened 9 years ago by Runsheng
  1

• improve GO and DO enrichment for GTEx papers?

  #6 opened 9 years ago by dalloliogm
  4