mpc-bioinformatics McQuaC issues

mpc-bioinformatics / McQuaC

Transform the Quality Control workflow from Knime into a workflow in Nextflow

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issues

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Retention time for spike-ins

#96 KarinSchork opened 3 days ago
2
charge of features should be given as relative instead of absolute number

#95 KarinSchork opened 3 days ago
1
consistency in naming of columns

#94 KarinSchork opened 3 days ago
0
remove TIC and basepeak up to 105 minutes

#93 KarinSchork opened 3 days ago
4
NF Cloud file names

#92 ChillerMango opened 4 days ago
0
TIC quartiles dont add up to 1 for short Bruker runs

#91 KarinSchork opened 1 week ago
0
SPIKE_..._RT_at_Maximum_Intensity = -1 if run is shorter than the expected retention time

#90 KarinSchork opened 1 week ago
3
QC Measure: New Plot: Ion Mobility Map for Bruker data

#89 Luxxii opened 3 weeks ago
1
Peak Width and also Datapoints per peak (average, or even quantiles of it)

#88 Luxxii opened 3 weeks ago
1
New Plot qc measure: Heatmap / Distributiuon of MS1 charges (disregarding the information from MS2)

#87 Luxxii closed 2 weeks ago
0
Bruker Files only get converted one after another (and not all at once)

#86 Luxxii opened 3 weeks ago
5
Changed CSV Output to HDF5 Output

#85 Luxxii opened 4 weeks ago
5
quality_control.csv is not assembled correctly on restructure branch

#84 di-hardt closed 1 month ago
1
Change CSV Outputs to a more suitable format (HDF5)

#83 Luxxii opened 1 month ago
0
Parameterize begin of cleaning step

#82 di-hardt closed 2 weeks ago
1
RT problems in the summary table

#81 SvitiMPC opened 1 month ago
1
Feature restructure Fixing #66, exposing columns to solve #69 and added new Column "ppm-error"

#80 Luxxii closed 1 month ago
2
Make repo "executable" via Nextflow

#79 julianu opened 1 month ago
0
Spike-ins in Bruker data?

#78 KarinSchork closed 1 month ago
3
TIMSTof: plot intensities of calibrants over time

#77 KarinSchork opened 1 month ago
1
Somethings wrong with

#76 di-hardt closed 1 month ago
1
FLI: the summary table is not updated

#75 SvitiMPC closed 1 month ago
1
Central Configuration file (for machines?)

#74 Luxxii opened 2 months ago
1
Remove msgf+ search parameters. (in restructuring)

#73 Luxxii closed 1 month ago
0
TimsToF: no figures are generated

#72 SvitiMPC closed 2 weeks ago
3
Question: is it possible to ignore the corrupted data?

#71 SvitiMPC closed 2 weeks ago
4
clean up work folder after execution

#70 KarinSchork opened 2 months ago
2
Ionmaps not aggregated

#69 julianu opened 2 months ago
12
PCA in square form not rectangle

#68 di-hardt closed 3 days ago
3
Add parameter weight to PCA

#67 di-hardt opened 3 months ago
4
Max TIC is missing

#66 di-hardt closed 2 months ago
6
Optional input: Peptide mass tolerance

#65 di-hardt closed 4 weeks ago
3
User question: Protein column

#64 di-hardt opened 3 months ago
3
Create separate comet file for TIM

#63 di-hardt opened 3 months ago
1
rename table 0 and change column order

#62 KarinSchork closed 2 months ago
0
Basepeak and total ion current identical?

#61 KarinSchork closed 2 weeks ago
7
Separate Settings for TIM?

#60 KarinSchork closed 2 months ago
1
Order of columns in table0

#59 KarinSchork opened 3 months ago
2
extract base peak information into table0

#58 KarinSchork closed 3 months ago
1
Fixing Comet Parameters and Caluclationof Spike In Information

#57 Luxxii closed 2 months ago
6
remove the fasta_datbases folder

#56 julianu closed 1 month ago
0
comet params changes

#55 julianu closed 2 months ago
1
Handling of spike in peptide results

#54 KarinSchork closed 3 months ago
0
Workflow to combine multiple QC result files

#53 KarinSchork closed 2 weeks ago
0
Rename Repo to McQuaC

#52 MaikeWeb closed 5 days ago
1
fixed analysis_timestamp

#51 KarinSchork closed 3 months ago
0
Spikein protein columns in quality-control.csv

#50 di-hardt closed 3 months ago
2
fix error when procesing non ISA files

#49 di-hardt closed 3 months ago
5
Documentation of how to setup this workflow in nf-cloud so that others can execute them on their own.

#48 Luxxii closed 1 month ago
2
YYYY_MM_DD is not correctly reported in the qc table

#47 Luxxii closed 3 months ago
0