Issues · bioinfo / ngs_tools · GitLab

MS worflow: improvements

#59 · created Jul 17, 2019 by domingue
- CLOSED
- 10
updated Aug 07, 2019
dge workflow: add GTF an argument for differential gene expression

#57 · created Jun 20, 2019 by domingue rna_seq
- 2
updated Jun 28, 2019
dge_workflow: error message because gtf_file did not exist

#58 · created Jun 27, 2019 by herseman
- CLOSED
- 1
updated Jun 27, 2019
dge_workflow: echoing R code in to Rscript not loading personal library packages

#56 · created Jun 19, 2019 by domingue rna_seq
- CLOSED
- 2
updated Jun 20, 2019
dge_workflow: include MA plot from ggpubr in dge report

#55 · created Jun 07, 2019 by herseman
- CLOSED
- 1
updated Jun 18, 2019
general: create templates for R scripts and shinyApps and revise the dge_star_template

#50 · created May 10, 2019 by herseman
- 1
updated May 14, 2019
general: fix issues which occur due to updated R package versions

#48 · created Apr 03, 2019 by herseman
- CLOSED
- 1
updated Apr 09, 2019
general: create new human igenome for the Ensembl release 95

#49 · created Apr 05, 2019 by herseman
- CLOSED
- 1
updated Apr 05, 2019
sc_workflow: add shinyApp to explore Seurat clusterings

#47 · created Mar 20, 2019 by herseman
- CLOSED
- 5
updated Mar 22, 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
sc_workflow: update sc_quality_check.R

#42 · created Feb 28, 2019 by herseman
- CLOSED
- 4
updated Mar 20, 2019
sc_workflow: write ShinyApp to explore metrics from the initial quality control

#44 · created Mar 04, 2019 by herseman
- CLOSED
- 3
updated Mar 20, 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
sc_workflow: add additional gene information for the top50 most highly abundant features in `sc_quality_check.R`

#46 · created Mar 13, 2019 by herseman
- CLOSED
- 1
updated Mar 13, 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
better handling of outliers

#17 · created May 30, 2017 by brandl
- CLOSED
- 0
updated Mar 07, 2019
Change bam_qc to report multi/single mapper proportions relative to number of aligned reads.

#13 · created May 18, 2017 by brandl
- CLOSED
- 0
updated Mar 07, 2019
add frip statistic to cs-workflow

#5 · created Mar 18, 2016 by brandl
- CLOSED
- 1
updated Mar 07, 2019
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

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