smith-chem-wisc/MetaMorpheus issues and pull requests

#2337 - Invert qvalue calculation

Pull Request - State: open - Opened by trishorts 5 months ago - 1 comment

#2336 - Add leucine to chymotrypsin cleavage motifs

Pull Request - State: open - Opened by trishorts 6 months ago - 1 comment
Labels: Bug, ready for review

#2335 - Specify contaminants database via command line

Issue - State: closed - Opened by mgraeff 6 months ago

#2334 - #1 - Update Mzlib to 1.0.548 (Omics Update)

Pull Request - State: open - Opened by nbollis 6 months ago - 1 comment
Labels: ready for review

#2333 - Custom mod on custom amino acid

Issue - State: open - Opened by lonelu 6 months ago - 1 comment

#2332 - No Effect from Including spectrumLibrary.msp

Issue - State: open - Opened by yuz2011 6 months ago

#2331 - Index was outside the bounds of the array

Issue - State: open - Opened by animesh 6 months ago

#2330 - Metadraw crashes with PSMs that contains the fixed modification "Arginine amide on R, prot C-termini" Uniprot

Issue - State: open - Opened by studentDenmark 6 months ago

#2329 - Andromeda score

Pull Request - State: open - Opened by trishorts 6 months ago
Labels: New Feature, WIP

#2328 - separation type menu not populated in calibration task window

Issue - State: open - Opened by trishorts 6 months ago

#2327 - Invert qvalue calculation

Pull Request - State: closed - Opened by trishorts 6 months ago - 1 comment
Labels: New Feature, ready for review

#2326 - Hide download proteome button

Pull Request - State: closed - Opened by trishorts 7 months ago

#2325 - Hydroxy proline diagnostic ion error

Pull Request - State: closed - Opened by trishorts 7 months ago
Labels: Bug

#2324 - Hydroxy proline diagnostic ion error

Pull Request - State: closed - Opened by trishorts 7 months ago
Labels: Bug

#2323 - MetaDraw doesn't load Looplinks or Deadends from crosslink search

Issue - State: open - Opened by trishorts 7 months ago

#2322 - N-glyco search improvements

Pull Request - State: open - Opened by trishorts 7 months ago - 1 comment
Labels: Bug, ready for review

#2321 - bug fix Modification Info List which reports the the modification stoichiometry in PSM counts and fractions on the full protein sequence

Pull Request - State: closed - Opened by trishorts 7 months ago - 1 comment
Labels: Bug

#2319 - [WIP] Enable saving of multiple settings for tasks

Pull Request - State: open - Opened by kscdnw 7 months ago - 1 comment

#2318 - Mzlib Update to 1.0.542 - Averaging crash fix+

Pull Request - State: closed - Opened by nbollis 8 months ago - 3 comments
Labels: Crash, ready for review, dependencies

#2317 - Glyco Visualization Crash Fix on ambiguous protein from peptide

Pull Request - State: closed - Opened by nbollis 8 months ago - 1 comment
Labels: Crash, Bug, Maintenance, ready for review

#2316 - Peptide centric search

Pull Request - State: open - Opened by trishorts 8 months ago
Labels: WIP

#2315 - peptide centric

Pull Request - State: open - Opened by YulingDai 8 months ago

#2314 - Removed 131C ions from TMT10

Pull Request - State: closed - Opened by Alexander-Sol 8 months ago

#2313 - MetaDraw Update: Font size increase, loading speed up, peak annotation display change

Pull Request - State: closed - Opened by nbollis 9 months ago - 1 comment
Labels: GUI, Performance, Maintenance, ready for review

#2312 - Crosslink user controlled protein N-terminal as a modification site

Issue - State: open - Opened by lonelu 10 months ago - 1 comment

#2311 - Added zPlusOne to custom ion selection

Pull Request - State: closed - Opened by nbollis 10 months ago - 1 comment
Labels: GUI, New Feature, ready for review

#2310 - Added SpectralAveraging.dll to project.wxs

Pull Request - State: closed - Opened by nbollis 10 months ago
Labels: Crash, Bug, ready for review, dependencies

#2309 - Glycopeptide label free quantification LFQ

Pull Request - State: closed - Opened by trishorts 10 months ago - 1 comment
Labels: ready for review

#2308 - 2267

Pull Request - State: closed - Opened by trishorts 10 months ago

#2307 - Hid Averaging Task Button until reason for crash is determined

Pull Request - State: closed - Opened by nbollis 10 months ago

#2306 - glyco spectrum library stuff

Issue - State: open - Opened by trishorts 10 months ago

#2305 - Fix string split in glyco protein parsimony

Pull Request - State: closed - Opened by trishorts 10 months ago - 1 comment

#2304 - Updated to MzLib 1.0.541 and updated one unit test

Pull Request - State: closed - Opened by nbollis 10 months ago
Labels: Performance, ready for review

#2303 - Ms2scan with specific mass eliminate unused code

Pull Request - State: closed - Opened by trishorts 10 months ago

#2302 - Trying to reduce the memory footprint of GPTMD and also speed it up

Pull Request - State: closed - Opened by trishorts 11 months ago - 3 comments
Labels: Maintenance, ready for review

#2301 - MetaMorpheus GUI fluctuating between running and not responding

Issue - State: open - Opened by mcorder 11 months ago

#2300 - [WIP] Evalue for best peptides

Pull Request - State: open - Opened by trishorts 11 months ago

#2299 - Compute spectrum similarity in meta draw

Pull Request - State: closed - Opened by trishorts 11 months ago - 4 comments
Labels: Output Enhancement, GUI, New Feature

#2298 - [WIP ]Add tailor score -NOT AN ACTUAL PR

Pull Request - State: open - Opened by trishorts 11 months ago

#2297 - Changed the main window to own the subsequent windows

Pull Request - State: closed - Opened by nbollis 11 months ago
Labels: Bug, GUI, User-Friendliness, ready for review

#2296 - Clean matched ion string glyco for MS3 in glyco

Pull Request - State: closed - Opened by trishorts 12 months ago - 1 comment

#2295 - Write spectrum library from PsmTsv in MetaDraw

Pull Request - State: closed - Opened by trishorts 12 months ago - 3 comments
Labels: New Feature, WIP

#2294 - Eliminate PEP from FDR analysis during calibration

Pull Request - State: closed - Opened by trishorts 12 months ago - 1 comment
Labels: Maintenance

#2293 - [WIP] Inverted q-value calculation

Pull Request - State: closed - Opened by trishorts almost 1 year ago
Labels: Performance, WIP

#2292 - Xl spectral library

Pull Request - State: closed - Opened by Alexander-Sol about 1 year ago - 1 comment
Labels: ready for review, ready for final review+merge

#2291 - Update Spectral Library Bug

Issue - State: open - Opened by nbollis about 1 year ago
Labels: Crash, Bug

#2290 - Added null checks to enable display of XL results

Pull Request - State: closed - Opened by Alexander-Sol about 1 year ago - 2 comments
Labels: Bug, ready for final review+merge

#2289 - XL toml causes crash

Issue - State: open - Opened by Alexander-Sol about 1 year ago

#2288 - In PTM search assigned unimod id dosen't match real unimod id

Issue - State: open - Opened by Nate4499 about 1 year ago

#2287 - Getting an "Arithmetic operation resulted in an overflow" error when calibrating the data

Issue - State: open - Opened by MKatWIS about 1 year ago

#2286 - [WIP] Multiplex reporting

Pull Request - State: open - Opened by Alexander-Sol about 1 year ago - 1 comment
Labels: WIP

#2285 - Filtering refactor

Pull Request - State: closed - Opened by Alexander-Sol about 1 year ago - 1 comment
Labels: ready for review

#2284 - Array.BinarySearch Audit

Issue - State: open - Opened by avcarr2 about 1 year ago - 2 comments

#2283 - XL-MS output ought to include two scan number columns to support MS3 identification?

Issue - State: open - Opened by hbarsnes about 1 year ago

#2282 - Database download Test

Pull Request - State: closed - Opened by elaboy about 1 year ago - 1 comment

#2281 - Averaging task in MetaMorpheus

Pull Request - State: closed - Opened by nbollis about 1 year ago - 1 comment
Labels: New Feature, ready for review

#2280 - Spectral library refactor

Pull Request - State: closed - Opened by Alexander-Sol about 1 year ago - 2 comments

#2279 - Spectral library generation writes dubious spectra

Issue - State: open - Opened by Alexander-Sol about 1 year ago

#2278 - Added additionaly support for tmt labeling

Pull Request - State: closed - Opened by Alexander-Sol about 1 year ago - 1 comment
Labels: New Feature, ready for review

#2277 - Added option to quantify ambiguous peptides

Pull Request - State: open - Opened by Alexander-Sol about 1 year ago - 1 comment
Labels: New Feature, WIP

#2276 - Update to MzLib 1.0.539

Pull Request - State: closed - Opened by nbollis about 1 year ago - 1 comment
Labels: ready for final review+merge, dependencies

#2275 - Ambiguous quant option

Pull Request - State: closed - Opened by Alexander-Sol about 1 year ago

#2274 - Ethcd complementary ions

Pull Request - State: closed - Opened by trishorts about 1 year ago - 1 comment
Labels: New Feature, ready for review

#2273 - Spectral recovery update

Pull Request - State: open - Opened by Alexander-Sol about 1 year ago - 1 comment

#2272 - [IGNORE] 1.0.2 final commit with mzLib 5.0.39 to get install artifact

Pull Request - State: closed - Opened by nbollis about 1 year ago

#2271 - Fw save settings

Pull Request - State: closed - Opened by nbollis about 1 year ago

#2270 - Spectra file connections aren't closed when the file is deleted from the Spectra tab

Issue - State: open - Opened by Alexander-Sol about 1 year ago - 1 comment

#2269 - Spectral recovery

Pull Request - State: closed - Opened by Alexander-Sol about 1 year ago - 1 comment
Labels: User-Friendliness, ready for final review+merge

#2268 - quant keeps going back to LFQ

Issue - State: open - Opened by jessegmeyerlab about 1 year ago - 1 comment

#2267 - Glyco flash

Pull Request - State: closed - Opened by trishorts over 1 year ago - 1 comment

#2266 - Glyco child scan display bugfix - Visualization Update Rebase

Pull Request - State: closed - Opened by nbollis over 1 year ago - 1 comment
Labels: Crash, Bug, GUI, ready for review

#2265 - should we have file specific normalized collision energy NCE

Issue - State: open - Opened by trishorts over 1 year ago
Labels: New Feature

#2264 - New uniprot

Pull Request - State: closed - Opened by Jevs242 over 1 year ago - 2 comments

#2263 - Updated mzLib to 1.0.538

Pull Request - State: closed - Opened by Alexander-Sol over 1 year ago

#2262 - Max quant reader

Pull Request - State: open - Opened by Alexander-Sol over 1 year ago

#2261 - Reverted filtering method for psms passed to FlashLFQ

Pull Request - State: closed - Opened by Alexander-Sol over 1 year ago - 2 comments

#2260 - Uniprot api update

Pull Request - State: closed - Opened by Jevs242 over 1 year ago - 4 comments

#2259 - [WIP] filter psms for flashlfq only by qvalue and qvalue notch

Pull Request - State: open - Opened by trishorts over 1 year ago - 1 comment
Labels: Bug, WIP

#2258 - [WIP] Unit Tests for LFQ in MetaMorpheus

Pull Request - State: open - Opened by trishorts over 1 year ago
Labels: Bug, Validation, Long-Term Stability, Maintenance, dependencies, WIP

#2257 - Download Proteome Error

Issue - State: closed - Opened by conorjenkins over 1 year ago - 3 comments

#2256 - Error Reading Experimental Design File when Re-Running a Search

Issue - State: open - Opened by conorjenkins over 1 year ago

#2255 - "Enhanced MBR" under LFQ isn't saved to .toml

Issue - State: closed - Opened by Alexander-Sol over 1 year ago - 2 comments

#2254 - Changed Target Architecture to x64

Pull Request - State: open - Opened by Alexander-Sol over 1 year ago - 1 comment
Labels: Maintenance

#2253 - Version 1.0.1 doesn't install runtimes on upgrade

Issue - State: open - Opened by CEBoos over 1 year ago

#2252 - Glyco write individual file results

Pull Request - State: closed - Opened by trishorts over 1 year ago - 2 comments
Labels: Output Enhancement, New Feature

#2251 - Add Bayesian Fold Change Analysis from FlashLFQ

Issue - State: open - Opened by trishorts over 1 year ago

#2250 - running on hpc environment

Issue - State: open - Opened by rsalz over 1 year ago - 7 comments

#2249 - Dont count diagnostic ions in MetaMorpheus Score or XCorr

Pull Request - State: closed - Opened by trishorts over 1 year ago - 1 comment
Labels: Bug, ready for review

#2248 - Allow decimal numbers for precursor and product mass tolerance in all tasks

Pull Request - State: closed - Opened by trishorts over 1 year ago
Labels: Bug, Input Enhancement, ready for review, WIP

#2247 - Unchecking "Overwrite App Data" during install causes crash on start

Issue - State: open - Opened by Alexander-Sol over 1 year ago

#2246 - Unchecking "Overwrite App Data" during install causes crash on start

Issue - State: closed - Opened by Alexander-Sol over 1 year ago

#2245 - Unchecking "Overwrite App Data" during install causes crash on start

Issue - State: closed - Opened by Alexander-Sol over 1 year ago

#2244 - Unchecking "Overwrite App Data" during install causes crash on start

Issue - State: closed - Opened by Alexander-Sol over 1 year ago

#2243 - Unchecking "Overwrite App Data" during install causes crash on start

Issue - State: closed - Opened by Alexander-Sol over 1 year ago

#2242 - Installer fix

Pull Request - State: closed - Opened by Alexander-Sol over 1 year ago

#2241 - I think there are configuration problems with the release so deleting ARM64 and x86

Pull Request - State: closed - Opened by trishorts over 1 year ago - 1 comment

#2240 - Cannot add Decimal Point in Product Mass Tolerance Box

Issue - State: closed - Opened by conorjenkins over 1 year ago - 4 comments

#2239 - we might be counting diagnostic ions in score for TMT and we probably shouldn't be

Issue - State: open - Opened by trishorts over 1 year ago

#2238 - Removing broken conda badge from readme

Pull Request - State: closed - Opened by acesnik over 1 year ago
Labels: ready for final review+merge

#2237 - Visualization Updates

Pull Request - State: closed - Opened by nbollis over 1 year ago - 1 comment
Labels: Bug, ready for review

GitHub / smith-chem-wisc/MetaMorpheus issues and pull requests