s-andrews/SeqMonk

Issues

• binary distribution for seqMonk

  #278 opened 3 months ago by iranianuser
  3

• Vistory event for Gene Set Enrichment

  #277 opened 6 months ago by ChristelKrueger
  1

• Gene Set Analysis picks up the wrong columns from MSigDB GMT files

  #276 opened 7 months ago by s-andrews
  1

• Building Custom Genome/Working with published genome

  #275 opened 7 months ago by riyabelani
  1

• Contig probe generator does not use strand information

  #274 opened 9 months ago by ChristelKrueger
  0

• Issue when lowering threshold difference with EdgeR on methylation data

  #273 opened 9 months ago by dsimps1993
  2

• Having trouble isolating hyper/hypomethylating probes after EdgeR

  #272 opened 9 months ago by dsimps1993
  3

• Blank column in Quantitation Trend Plot Output

  #266 opened a year ago by StevenWingett
  2

• Installation in a linux/HPC R environment

  #268 opened a year ago by robin-sto
  1

• How to upload annotations without webserver connection?

  #270 opened a year ago by KristenKrolick
  2

• Unchanged data stores create vistory event upon 'replace in name'

  #271 opened a year ago by ChristelKrueger
  0

• issue with proxy server

  #269 opened a year ago by periv4
  5

• When customizing a genome, the regionname in the fasta file is not read correctly

  #267 opened a year ago by Shokusei
  2

• Add flexibility to the exact overlap quantitation

  #265 opened 2 years ago by s-andrews
  0

• EdgeR for/rev doesn't work with volcano plot

  #264 opened 2 years ago by s-andrews
  0

• Add filter or warning to EdgeR for/rev

  #263 opened 2 years ago by s-andrews
  0

• Change default for variation plot to be STDEV

  #262 opened 2 years ago by s-andrews
  0

• Description/Help for duplication plot

  #261 opened 2 years ago by ChristelKrueger
  0

• Inverted colours when running via XQuartz on M1 macs

  #260 opened 2 years ago by s-andrews
  1

• formatting of Quantitation Trend Plot data table

  #259 opened 3 years ago by ChristelKrueger
  0

• Memory auto-detection fails on new OSX machines

  #257 opened 3 years ago by s-andrews
  2

• Launch script fails to detect 64 bit OS if java is not in the path

  #258 opened 3 years ago by s-andrews
  0

• Support for M1 ARM based Mac systems

  #251 opened 3 years ago by s-andrews
  5

• Don't allow failed loads to go into the recently loaded files

  #252 opened 3 years ago by s-andrews
  1

• Network connectivity issue with Java

  #256 opened 3 years ago by tthompson29
  5

• GFF3 annotation export in SeqMonk

  #253 opened 3 years ago by hidvegin
  1

• Vistory entry for renaming features

  #255 opened 3 years ago by ChristelKrueger
  0

• Vistory entry for Define Probes -> Create Annotation Track

  #254 opened 3 years ago by ChristelKrueger
  0

• Crash reports not sending?

  #250 opened 4 years ago by s-andrews
  0

• Support CellRanger-style sampleID within readID

  #249 opened 4 years ago by FelixKrueger
  6

• Crash when switching orientations in beanplot and boxplot

  #248 opened 4 years ago by s-andrews
  2

• All JDialog based windows cause hang on Big Sur OSX

  #247 opened 4 years ago by s-andrews
  2

• seqmonk_import doesn't detect java

  #245 opened 4 years ago by s-andrews
  0

• New bioconductor breaks on anything older than R4.0.3

  #246 opened 4 years ago by s-andrews
  0

• Add another OSX R location to check

  #244 opened 4 years ago by s-andrews
  1

• Problems running SeqMonk on a cluster, 'open3 error'

  #241 opened 4 years ago by AlexBlais74
  16

• Crash if DESeq p-value is removed

  #243 opened 4 years ago by s-andrews
  2

• Provide some support for circular genomes

  #242 opened 4 years ago by s-andrews
  0

• Feature Request: Options for directories on startup

  #232 opened 4 years ago by code4dna
  2

• Is SeqMonk able to analyse methylations on PacBio RSII chem?

  #239 opened 4 years ago by camilogarciabotero
  1

• Which output file of bismark methylation calls to use as the input file of seqmonk ？

  #240 opened 4 years ago by akui113
  2

• Feature cache doesn't update properly when a feature is renamed

  #238 opened 4 years ago by s-andrews
  0

• SeqMonk won't launch on OSX <10.14

  #237 opened 4 years ago by s-andrews
  1

• Crash when reading cached genomes in seqmonk_import

  #236 opened 4 years ago by s-andrews
  0

• Install failures on R3.6.x due to missing XML

  #233 opened 4 years ago by s-andrews
  0

• Improvements to gene set enrichment results

  #235 opened 4 years ago by s-andrews
  0

• Improvements to the probe list overlap plot

  #234 opened 4 years ago by s-andrews
  0

• Still getting prompted by R to install from source

  #231 opened 4 years ago by s-andrews
  1

• Make nicer OSX dmg installer

  #229 opened 4 years ago by s-andrews
  3

• Allow creating new annotations from multiple probe lists

  #228 opened 4 years ago by s-andrews
  0