RforMassSpectrometry/Spectra issues and pull requests

#330 - Improve and fix the Spectra constructor method

Pull Request - State: closed - Opened by jorainer 19 days ago - 1 comment

#329 - feat: add a function to coerce from Spectra to MSnbase::MSpectra

Pull Request - State: closed - Opened by jorainer 21 days ago - 1 comment

#328 - Change estimatePrecursorIntensity to a method

Pull Request - State: closed - Opened by jorainer 2 months ago

#327 - Interpretation of matchSpectra() and plotting results of plotSpectraMirror()

Issue - State: open - Opened by v-v1150n 3 months ago

#326 - feat: add new `filterPeaksRanges` function

Pull Request - State: closed - Opened by jorainer 3 months ago - 2 comments

#325 - Coerce Spectra to DataFrame

Issue - State: closed - Opened by lgatto 3 months ago - 3 comments

#324 - adduct type

Issue - State: open - Opened by cbroeckl 4 months ago - 1 comment

#323 - Add a method to change the data storage base path for on-disk backends

Pull Request - State: closed - Opened by jorainer 5 months ago

#322 - MS-imaging support / MsBackendImzML

Issue - State: open - Opened by RogerGinBer 5 months ago - 3 comments

#321 - Add possibility to change the file path for a `MsBackendMzR`

Issue - State: closed - Opened by jorainer 5 months ago - 2 comments

#103 - other: [email protected] is maintainer

Pull Request - State: closed - Opened by lgatto over 4 years ago

#102 - Replace the `clean` method with `filterIntensity` (issue #89)

Pull Request - State: closed - Opened by jorainer over 4 years ago - 1 comment

#101 - refactor: replace removePeaks with replaceIntensitiesBelow

Pull Request - State: closed - Opened by jorainer over 4 years ago - 1 comment

#100 - Add/fix github actions

Issue - State: closed - Opened by jorainer over 4 years ago - 2 comments

#99 - fix: support import of mzML files with different header columns

Pull Request - State: closed - Opened by jorainer over 4 years ago - 1 comment

#98 - Add containsMz and containsNeutralLoss

Pull Request - State: closed - Opened by jorainer over 4 years ago - 1 comment

#97 - refactor: import ndotproduct instead of dotproduct from MsCoreUtils

Pull Request - State: closed - Opened by jorainer over 4 years ago - 2 comments

#96 - hasMz or containsMz

Issue - State: closed - Opened by michaelwitting over 4 years ago - 5 comments

#95 - spectraData,Spectra does not return m/z and intensity values

Pull Request - State: closed - Opened by jorainer over 4 years ago - 2 comments

#94 - refactor: mz and intensity aren't part of the default spectraVariables anymore

Pull Request - State: closed - Opened by lgatto over 4 years ago - 2 comments

#93 - Backends for the meta-data

Issue - State: closed - Opened by lgatto over 4 years ago - 6 comments

#92 - spectraData pulls mz and intenstities

Issue - State: closed - Opened by lgatto over 4 years ago - 20 comments

#90 - Some wording improving removePeaks() and clean()

Pull Request - State: closed - Opened by sneumann over 4 years ago - 2 comments

#89 - optimize function names (removePeaks, clean)

Issue - State: closed - Opened by schymane over 4 years ago - 14 comments

#88 - Drop spectra varibles that are only NA

Pull Request - State: closed - Opened by jorainer almost 5 years ago - 2 comments

#87 - Error: object ‘asRle’ is not exported by 'namespace:MsCoreUtils'

Issue - State: closed - Opened by cpanse almost 5 years ago - 2 comments

#86 - [API] Rename `as.list`?

Issue - State: closed - Opened by sgibb almost 5 years ago - 10 comments
Labels: question, API

#85 - Remove all functionality related to Rle-based compression

Pull Request - State: closed - Opened by jorainer almost 5 years ago - 4 comments

#84 - Evaluation rhdf5client to provide an remote HDF5 backend

Issue - State: open - Opened by sgibb almost 5 years ago - 20 comments
Labels: enhancement, backends

#83 - Remove the Rle-based compression

Issue - State: closed - Opened by jorainer almost 5 years ago - 1 comment

#82 - Error reading some data files

Issue - State: closed - Opened by jorainer almost 5 years ago - 1 comment

#81 - Dropping spectra variables/columns containing only NA values

Issue - State: closed - Opened by jorainer almost 5 years ago - 6 comments

#80 - Add some basic plotting functions

Issue - State: closed - Opened by sgibb almost 5 years ago - 17 comments
Labels: enhancement, help wanted, good first issue

#79 - add MsCoreUtils remote

Pull Request - State: closed - Opened by lgatto almost 5 years ago

#78 - pickPeaks changes centroided status

Pull Request - State: closed - Opened by jorainer almost 5 years ago - 2 comments

#77 - pickPeaks does not change centroided

Issue - State: closed - Opened by jorainer almost 5 years ago
Labels: bug

#76 - Add Spectra,smooth

Pull Request - State: closed - Opened by sgibb almost 5 years ago - 1 comment

#75 - Add combineSpectra

Pull Request - State: closed - Opened by jorainer almost 5 years ago - 1 comment

#74 - Add a `combineSpectra` equivalent method

Issue - State: closed - Opened by jorainer almost 5 years ago

#73 - refactor: use dotproduct as default function to compare spectra

Pull Request - State: closed - Opened by jorainer almost 5 years ago - 2 comments

#72 - refactor: replace `peaks` method with `as.list` (issue #62)

Pull Request - State: closed - Opened by jorainer about 5 years ago - 2 comments

#71 - refactor: changes addressing performance bottlenecks

Pull Request - State: closed - Opened by jorainer about 5 years ago - 4 comments

#70 - show,ProcessingStep isn't working if FUN is a function

Issue - State: closed - Opened by sgibb about 5 years ago - 1 comment
Labels: bug

#69 - feat: Add `split,MsBackend` and `split,Spectra`

Pull Request - State: closed - Opened by jorainer about 5 years ago - 2 comments

#68 - backendMerge,MsBackendDataFrame very slow

Issue - State: closed - Opened by jorainer about 5 years ago - 1 comment

#67 - MsBackendMzR: don't import core spectra variables with only NA

Issue - State: closed - Opened by jorainer about 5 years ago

#66 - Add split,Spectra

Issue - State: closed - Opened by jorainer about 5 years ago

#65 - feat: Add `lapply,Spectra`

Pull Request - State: closed - Opened by jorainer about 5 years ago

#64 - Better/faster subsetting of MsBackendDataFrame

Issue - State: closed - Opened by jorainer about 5 years ago - 2 comments

#63 - Some refactoring

Pull Request - State: closed - Opened by jorainer about 5 years ago - 6 comments

#62 - Replace peaks method by as.list

Issue - State: closed - Opened by jorainer about 5 years ago - 4 comments

#61 - Define an endoapply and lapply method

Issue - State: closed - Opened by jorainer about 5 years ago - 3 comments

#60 - Remove Rle-based compression utilities and import them from MsCoreUtils

Pull Request - State: closed - Opened by jorainer about 5 years ago - 1 comment

#59 - Import Rle related utilities from MsCoreUtils

Issue - State: closed - Opened by jorainer about 5 years ago

#58 - Remove parameter ppm from filterPrecursorMz and code cleanup

Pull Request - State: closed - Opened by jorainer about 5 years ago - 5 comments

#57 - change filterPrecursorMz to accept an m/z range

Issue - State: closed - Opened by jorainer about 5 years ago - 4 comments

#56 - Import bin from MsCoreUtils

Issue - State: closed - Opened by jorainer about 5 years ago

#55 - Update to ProtGenerics 1.17.4

Pull Request - State: closed - Opened by jorainer about 5 years ago - 1 comment

#54 - Reduce a few `peaks` calls in `compare_spectra*`

Pull Request - State: closed - Opened by sgibb about 5 years ago - 1 comment

#53 - Add joinPeaks and compareSpectra

Pull Request - State: closed - Opened by jorainer about 5 years ago - 3 comments

#52 - Add pickPeaks method

Pull Request - State: closed - Opened by sgibb about 5 years ago - 2 comments

#51 - Add favicon to pkgdown site

Pull Request - State: closed - Opened by sgibb about 5 years ago - 1 comment
Labels: documentation

#50 - import MsCoreUtils

Pull Request - State: closed - Opened by lgatto about 5 years ago - 5 comments

#49 - align/match peaks of two `Spectrum` objects

Issue - State: open - Opened by tnaake about 5 years ago - 6 comments

#48 - Add compareSpectra and re-use binning from MsCoreUtils

Pull Request - State: closed - Opened by jorainer about 5 years ago - 2 comments

#47 - Replace vapply by MsCoreUtils::vapply1{c,d,l}

Pull Request - State: closed - Opened by sgibb about 5 years ago

#46 - compareSpectra,Spectra,Spectra

Issue - State: closed - Opened by jorainer about 5 years ago - 22 comments
Labels: question

#45 - Add matchApprox utility function

Pull Request - State: closed - Opened by jorainer about 5 years ago - 5 comments

#44 - Bypass .peaksapply if processing queue is empty

Issue - State: closed - Opened by jorainer over 5 years ago - 2 comments

#43 - Add the `bin,Spectra` method

Pull Request - State: closed - Opened by jorainer over 5 years ago - 1 comment

#40 - Add applyProcessing function

Pull Request - State: closed - Opened by jorainer over 5 years ago

#39 - Replace `@files` with `dataStorage` and `dataOrigin`

Pull Request - State: closed - Opened by jorainer over 5 years ago - 4 comments

#38 - Require rt to be of length 2 in filterRt

Pull Request - State: closed - Opened by lgatto over 5 years ago - 5 comments

#37 - What is the unit for rtime? Minutes or seconds?

Issue - State: closed - Opened by cpanse over 5 years ago - 4 comments

#36 - travis ci

Issue - State: closed - Opened by sgibb over 5 years ago - 8 comments

#35 - .rbind_fill doesn't work if the first DataFrame doesn't contain a SimpleList but the second one

Pull Request - State: closed - Opened by sgibb over 5 years ago

#34 - Use {v,l}apply in .as_vector_spectra_data

Pull Request - State: closed - Opened by sgibb over 5 years ago - 1 comment

#33 - Use Rle in .as_rle whenever possible and useful

Pull Request - State: closed - Opened by sgibb over 5 years ago - 1 comment

#32 - Replacements for fromFile and fileNames

Issue - State: closed - Opened by jorainer over 5 years ago - 1 comment

#31 - Major pull request

Pull Request - State: closed - Opened by jorainer over 5 years ago - 2 comments

#30 - Add modCount and files as spectra variables

Issue - State: closed - Opened by jorainer over 5 years ago - 6 comments

#29 - Use `c` instead of `merge` to combine `Spectra`

Issue - State: closed - Opened by jorainer over 5 years ago

#28 - Rename fileNames to dataSource

Issue - State: closed - Opened by jorainer over 5 years ago - 8 comments

#27 - Topics for discussion

Issue - State: closed - Opened by jorainer over 5 years ago

#26 - Implement (internal or virtual?) backend with compressed DataFrame

Issue - State: closed - Opened by jorainer over 5 years ago - 6 comments

#25 - Add functionality to split and merge Spectra objects

Issue - State: closed - Opened by jorainer over 5 years ago - 1 comment

#24 - Add functionality to split and merge backends

Issue - State: closed - Opened by jorainer over 5 years ago

#23 - Add possibility to change the backend of a Spectra

Issue - State: closed - Opened by jorainer over 5 years ago - 3 comments

#22 - First working version of Spectra

Pull Request - State: closed - Opened by jorainer over 5 years ago - 2 comments

#21 - Add a filter function and AnnotationFilter filters

Issue - State: closed - Opened by jorainer over 5 years ago - 3 comments

#20 - Spectra interface

Issue - State: open - Opened by jorainer over 5 years ago - 2 comments

#19 - Add MsBackendDataFrame and MsBackendMzR

Pull Request - State: closed - Opened by jorainer over 5 years ago - 18 comments

#18 - Implement a MsBackendRleDataFrame

Issue - State: closed - Opened by jorainer over 5 years ago - 1 comment

#17 - Compare `BackendDataFrame` with `BackendRleDataFrame`

Issue - State: closed - Opened by jorainer over 5 years ago - 3 comments

#16 - Add implementations for MsBackendDataFrame and MsBackendMzR

Pull Request - State: closed - Opened by jorainer over 5 years ago - 2 comments

GitHub / RforMassSpectrometry/Spectra issues and pull requests