Issues · bioinfo / ngs_tools · GitLab

sc_workflow: add script for the calculation of diffusion map and pseudo time using the `destiny` package

#43 · created Mar 01, 2019 by herseman
- CLOSED
- 2
updated Mar 05, 2019
sc_workflow: update sc_quality_check.R

#42 · created Feb 28, 2019 by herseman
- CLOSED
- 4
updated Mar 20, 2019
ms_workflow: ms_limma.R returns error when no differentially abundant proteins were found

#41 · created Feb 14, 2019 by herseman mass_spec
- CLOSED
- 1
updated Feb 14, 2019
ms_workflow: handling of technical replicates

#40 · created Feb 13, 2019 by herseman mass_spec
- 2
updated Dec 09, 2019
general: create customized docker files for individual analyses done with our ngs_tools scripts

#39 · created Feb 11, 2019 by herseman
- 3
updated Mar 14, 2019
general: save the actually used ngs_tools script in results data folder

#38 · created Feb 11, 2019 by herseman
- CLOSED
- 7
updated Mar 13, 2019
ms_workflow: handling of contaminations

#37 · created Feb 08, 2019 by herseman mass_spec
- CLOSED
- 1
updated Dec 10, 2019
ms_workflow: add additional quality metrics to the differential abundance analysis output

#36 · created Feb 06, 2019 by herseman mass_spec
- CLOSED
- 3
updated Mar 08, 2019
sc_workflow: write single script for Seurat workflow with tested and approved settings

#35 · created Jan 16, 2019 by herseman
- 3
updated Mar 22, 2019
ms_workflow: report differential abundance proteins along with the identification type information as well as additional protein information

#34 · created Jan 15, 2019 by herseman
- CLOSED
- 1
updated Feb 01, 2019
ms_workflow: report settings from MaxQuant log file

#33 · created Jan 15, 2019 by herseman mass_spec
- CLOSED
- 2
updated Feb 12, 2019
ms_workflow: aggregate protein isoforms data on gene level

#32 · created Jan 15, 2019 by herseman mass_spec
- 0
updated Feb 08, 2019
ms_workflow: report number of peptides (unique and razor peptides) for each protein group

#31 · created Jan 15, 2019 by herseman mass_spec
- 2
updated Feb 08, 2019
ms_workflow: add option to run analysis on raw intensities instead of LFQs

#30 · created Jan 15, 2019 by herseman
- CLOSED
- 0
updated Jan 15, 2019
revise limma workflow for mass spec data

#29 · created Jan 10, 2019 by herseman
- CLOSED
- 1
updated Jan 11, 2019
ms_workflow: Improvemnts 7 of 9 tasks completed

#28 · created Dec 07, 2018 by brandl mass_spec
- CLOSED
- 3
updated Dec 10, 2019
new ticket

#27 · created Nov 15, 2018 by brandl 3h
- CLOSED
- 3
updated Dec 07, 2018
update to more recent https://github.com/deeptools/deepTools/releases

#26 · created Aug 16, 2018 by brandl 2h
- CLOSED
- 3
updated Feb 20, 2020
report improvements

#25 · created Nov 16, 2017 by brandl
- CLOSED
- 1
updated Feb 20, 2020
DESeq2 check current clustering method

#24 · created Nov 15, 2017 by herseman
- 0
updated Nov 29, 2018

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