rformassspectrometry/Spectra

Issues

• Check and fix backends for the new Spectra version

  #333 opened 3 months ago by jorainer
  1

• Issue with `MsBackendCompDb`

  #334 opened 3 months ago by philouail
  1

• Interpretation of matchSpectra() and plotting results of plotSpectraMirror()

  #327 opened 5 months ago by v-v1150n
  0

• Coerce Spectra to DataFrame

  #325 opened 5 months ago by lgatto
  3

• adduct type

  #324 opened 7 months ago by cbroeckl
  1

• MS-imaging support / MsBackendImzML

  #322 opened 7 months ago by RogerGinBer
  3

• Add possibility to change the file path for a `MsBackendMzR`

  #321 opened 7 months ago by jorainer
  2

• Suggesion for combinePeaksData

  #320 opened 7 months ago by DrRuiLi
  4

• Visualize, use plotSpectraMirror function to draw spectrum matching results

  #319 opened 8 months ago by v-v1150n
  1

• Adjust precursor m/z values for MS2 spectra from Waters instruments

  #315 opened 9 months ago by jorainer
  5

• Fix is.vector()

  #318 opened 9 months ago by lgatto
  3

• Smoothing along the time domain (chromatographic peaks)

  #316 opened 9 months ago by breidan
  1

• AnnotationFilter-based filtering of Spectra objects?

  #313 opened 10 months ago by jorainer
  3

• Add a method to calculate the entropy of all spectra

  #308 opened 10 months ago by jorainer
  1

• Problem with MGF import - object: mz values have to be sorted increasingly

  #311 opened 10 months ago by felipe-mansoldo
  3

• Problem with Waters raw file

  #310 opened a year ago by sardnar
  2

• Memory issues and (potential) chunk-wise processing of peaks data

  #304 opened a year ago by jorainer
  8

• Ensure all methods working on peaksData use the chunk-wise processing

  #307 opened a year ago by jorainer
  0

• `bin` function *create* peaks of intensity 0

  #303 opened a year ago by philouail
  4

• `filterFourierTransformArtefacts` fails when used with other processings

  #302 opened a year ago by Adafede
  4

• Add a filterPrecursorPeaks function

  #293 opened a year ago by jorainer
  5

• Add documentation on MS entropy-based similarity calculation

  #301 opened a year ago by jorainer
  4

• Add a filterUniquePrecursorMz method

  #280 opened a year ago by jorainer
  4

• Add a filterPrecursorIsotopes method

  #281 opened a year ago by jorainer
  4

• Import mspLib format

  #294 opened 2 years ago by Slycopersicum
  4

• Add scalePeaks function

  #291 opened 2 years ago by jorainer
  0

• Add fusePeaks function

  #292 opened 2 years ago by jorainer
  8

• New feature: group and summarised Spectra

  #295 opened 2 years ago by lgatto
  2

• API CHANGE: support peaksData to return data.frame or matrix

  #289 opened 2 years ago by jorainer
  11

• Add validator method to MsBackend checking for ordered m/z values

  #261 opened 2 years ago by jorainer
  2

• Add support for peak annotations

  #287 opened 2 years ago by jorainer
  0

• Split Spectra documentation into smaller chunks

  #288 opened 2 years ago by jorainer
  0

• Add a reduce method

  #282 opened 2 years ago by jorainer
  4

• Add a deisotope function

  #283 opened 2 years ago by jorainer
  0

• Version 1.8.x Spectra objects not readable by earlier package versions?

  #284 opened 2 years ago by AharoniLab
  2

• filterMzValues

  #274 opened 2 years ago by mar-garcia
  10

• "chunkyfied" processing

  #249 opened 2 years ago by jorainer
  2

• A tutorial and specification for building backends

  #262 opened 2 years ago by meowcat
  16

• Check if a backend supports parallel processing

  #271 opened 2 years ago by jorainer
  7

• MzBackendMzR misleading error with empty file list and misleading behavior with `files` argument

  #267 opened 2 years ago by meowcat
  3

• `setBackend` to `MsBackendMemory` fails for empty `Spectra`

  #268 opened 2 years ago by meowcat
  2

• Re-evaluate automatic detection of peaks variables

  #269 opened 2 years ago by jorainer
  1

• Function to find/visualise contaminants

  #260 opened 2 years ago by lgatto
  2

• pickPeaks fails to centroid if no flanking zeroes are present

  #257 opened 2 years ago by RogerGinBer
  4

• Externalize hdf5 backend?

  #264 opened 2 years ago by meowcat
  3

• Bug in containsMz()

  #258 opened 2 years ago by lgatto
  7

• filterPrecursorMzRange

  #256 opened 2 years ago by cbroeckl
  2

• An attempt to convert a spectra file to a data frame

  #251 opened 2 years ago by linlennypinawa
  7

• To extract method info from mzXML file(s)?

  #253 opened 2 years ago by linlennypinawa
  1

• compareSpectra inconsistency?

  #252 opened 2 years ago by Adafede
  4