Shians/Glimma

Issues

• Still written logCPM in expression description even when transform=FALSE

  #180 opened 9 months ago by amayer21
  0

• Toggle header for glimmaMDS depending on the gene.selection argument

  #179 opened 2 years ago by jmacdon
  0

• glimmaMDS/glimmaMD can't find local directories

  #177 opened 4 years ago by jdrnevich
  1

• Specifying a second grouping as batch effect

  #178 opened 4 years ago by peterleary
  0

• allow interactive plots in both RStudio and markdown reports

  #109 opened 8 years ago by mritchie
  3

• Table in glMDPlot not showing all columns

  #140 opened 7 years ago by jdrnevich
  5

• single-cell specific plots/options

  #108 opened 8 years ago by mritchie
  1

• Add volcano plot wrapper

  #166 opened 6 years ago by Shians
  1

• glXYPlot changing the count values from ExpressionSet object

  #145 opened 7 years ago by foramashar
  1

• Values are rounded incorrectly

  #175 opened 5 years ago by sam-israel
  0

• Allow sizes of sample expression points to change (maybe scale by sample weights)

  #167 opened 6 years ago by Shians
  0

• Multiple contrasts broken for DGELRT

  #169 opened 6 years ago by Shians
  0

• Allow x-axis label rotation in expressions plot of MD plot

  #171 opened 6 years ago by Shians
  0

• Allow expressions to only be stored for significant genes

  #172 opened 6 years ago by Shians
  0

• Allow fixing of y-axis in expression plot of MD plot

  #174 opened 6 years ago by Shians
  0

• glMDPlot output empty html

  #170 opened 6 years ago by u9090
  5

• Unable to set xlab argument using glMDPlot.MArrayLM()

  #114 opened 6 years ago by gaiatek
  12

• Unhelpful failure in glMDPlot when group is not a vector

  #163 opened 7 years ago by Shians
  0

• top option does not change glMDSPlot results

  #138 opened 6 years ago by mueggeb
  2

• glMDSplot should invisibly return MDS values

  #131 opened 7 years ago by jdrnevich
  3

• sample assignment incorrect in glMDPlot 1.8.1 vs. 1.6.0

  #164 opened 6 years ago by jdrnevich
  2

• bug in glMDPlot.default: internal function make_side_main_unique()

  #159 opened 7 years ago by jdrnevich
  1

• glMDPlot's transform argument description needs to be changed

  #160 opened 7 years ago by jdrnevich
  1

• Issue when side.main column contains NA

  #123 opened 7 years ago by Shians
  1

• glMDSPlot not doing gene.selection = "common" correctly

  #133 opened 7 years ago by jdrnevich
  1

• Export table from glMDPlot

  #122 opened 8 years ago by Shians
  1

• Add links to gene IDs and symbols

  #152 opened 7 years ago by Shians
  0

• Add gene list word cloud function

  #153 opened 7 years ago by Shians
  0

• Easy way to adjust order of groups in top right plot of glMDPlot?

  #148 opened 7 years ago by jdrnevich
  2

• Update the data table with custom zoom

  #155 opened 7 years ago by sejmodha
  0

• glMDplot changes numeric columns with NAs to character in bottom table

  #147 opened 7 years ago by jdrnevich
  2

• wrong assignment of ids to values in glMDPlot() HTML

  #146 opened 7 years ago by assafwww
  0

• Implement shared counts data

  #144 opened 7 years ago by Shians
  0

• Add handling for when anno is a vector

  #142 opened 7 years ago by Shians
  0

• Request and bug in P.Values in glMDPlot

  #139 opened 7 years ago by jdrnevich
  2

• Allow more groups on expressions plot

  #121 opened 8 years ago by Shians
  4

• Remove pop-up box when selecting points

  #125 opened 8 years ago by charitylaw
  0

• Incorrect adj.P.Vals in table of glMDPlot

  #124 opened 8 years ago by charitylaw
  5

• Continuous scale for MDS colours

  #120 opened 8 years ago by Shians
  0

• Legend for MDS Plot

  #119 opened 8 years ago by Shians
  1

• Request legend for MDS plot

  #118 opened 8 years ago by jdrnevich
  0

• Reduce footprint of data.js / increase speed

  #116 opened 8 years ago by vasiliosz
  1

• Proposed MDS plot

  #105 opened 8 years ago by charitylaw
  0

• extend plotting options

  #106 opened 8 years ago by mritchie
  0

• add other dimension reduction options

  #107 opened 8 years ago by mritchie
  0

• Cool Venn diagrams

  #104 opened 8 years ago by Shians
  0

• Let groups in counts plot be ordered the same as levels of factor

  #103 opened 8 years ago by Shians
  0

• Clicking MD plot points doesn't always scroll to gene properly

  #102 opened 8 years ago by Shians
  0

• Combine anon with fit$genes rather than replace

  #70 opened 8 years ago by Shians
  1

• Expressions plot points scaled by sample weight

  #64 opened 8 years ago by Shians
  0