iDEP-SDSU/idep

Issues

• Hierarchical clustering in sample tree?

  #229 opened a year ago by marwa38
  0

• size of gene names on heatmap idep 1.1?

  #228 opened a year ago by marwa38
  0

• specific genes statistical analysis?

  #227 opened a year ago by marwa38
  0

• scrol down is inctive?

  #226 opened a year ago by marwa38
  0

• list of genes/pathways for the type of genes or shared genes in venn diagram?

  #225 opened a year ago by marwa38
  0

• some suggestions

  #224 opened a year ago by marwa38
  0

• How do you caculate the normalized value in processed data

  #223 opened a year ago by lizhebio
  0

• Fission yeast gene error

  #121 opened a year ago by gexijin
  0

• DEG2 heatmap only showing part of the samples

  #124 opened a year ago by gexijin
  0

• iDEP for pathway analysis using GWAS genetic variants data

  #125 opened 3 years ago by Sithara85
  1

• New version of iDEP 0.95 slow on DEG2

  #192 opened a year ago by gexijin
  0

• Paper that utilised iDEP for RNAseq downstream analysis

  #222 opened a year ago by marwa38
  1

• DEG in IDEP 0.96 and IDEP 1.0

  #221 opened 2 years ago by ysuzuki1978
  0

• different annotation inputs?

  #220 opened 2 years ago by marwa38
  0

• "Diff_Chr_Regions_.csv" and "Genes_in_Diff_Chr_Regions_.csv" are not consistent to genome plot

  #219 opened 2 years ago by EikoSAIJOU334
  0

• Enhancement option: Ensembl genes ids into Human Gene Symbols?

  #217 opened 2 years ago by marwa38
  0

• volcano plot?

  #216 opened 2 years ago by marwa38
  0

• Using full EdgeR DEG analysis

  #215 opened 2 years ago by remybonnav
  0

• iDep execution in command line

  #214 opened 2 years ago by Luiky1
  0

• how can we have a color key scale in correlation matrix and K-means clustering?

  #203 opened 2 years ago by kamalmdmostafa
  3

• I have a problem about pathwayDB!

  #160 opened 2 years ago by luozhy88
  2

• Document how to add a new species to the database

  #131 opened 2 years ago by Akusem
  2

• Example Gene IDS produces error for mouse

  #169 opened 2 years ago by slsevilla
  1

• Background genes in iDEP

  #137 opened 2 years ago by gexijin
  0

• Transcript ID partially converted to genId

  #171 opened 2 years ago by ramay
  1

• What is "c.out"?

  #197 opened 2 years ago by repbio
  1

• Mixed types of gene ids in ShinyGO

  #187 opened 2 years ago by gexijin
  0

• Ngnix load balancer improvement

  #200 opened 2 years ago by gexijin
  0

• Export edge table from network tab

  #198 opened 2 years ago by palenic
  0

• Access to database 105 (iDEP 95 db)

  #170 opened 2 years ago by Akusem
  1

• Long pathway names in ShinyGO barchart

  #188 opened 2 years ago by gexijin
  1

• Could not connect to database: unable to open database file

  #168 opened 3 years ago by kamalmdmostafa
  1

• KEGG pathway not being displayed

  #167 opened 3 years ago by mgalland
  5

• Background excluded in ShinyGO

  #165 opened 3 years ago by Jelinek-J
  2

• Which method is used, either limma or DESeq2?

  #148 opened 3 years ago by wonwill
  1

• data dir not correct

  #164 opened 3 years ago by daaaaande
  1

• [ShinyGo] gene expression level?

  #162 opened 3 years ago by AgatioDev
  1

• TPM?

  #161 opened 3 years ago by AgatioDev
  2

• [BUG] High resolution figure download button not working in PCA > Pathway Analysis of PCA rotation

  #166 opened 3 years ago by Akusem
  1

• KEGG pathway diagram does not show up in iDEP 0.92

  #119 opened 3 years ago by gexijin
  2

• STRING API species dropdown menu?

  #158 opened 3 years ago by marwa38
  2

• Atlantic Salmon Ensembl?

  #140 opened 3 years ago by marwa38
  6

• Enhance human and mouse related gene network analysis

  #142 opened 3 years ago by gexijin
  0

• Give access to the last version of the database

  #130 opened 3 years ago by Akusem
  3

• Update install instruction

  #132 opened 3 years ago by Akusem
  1

• Error message when only one factor in design matrix

  #123 opened 3 years ago by gexijin
  1

• Disable DESeq2 for normalized expression data

  #122 opened 3 years ago by gexijin
  1

• Change colors in PCA plot

  #120 opened 3 years ago by gexijin
  0

• DESeq2 error without choosing factors

  #117 opened 3 years ago by gexijin
  1

• Limma not working when selecting comparisons

  #118 opened 3 years ago by gexijin
  0