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bioinfo
ngs_tools
Issues
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15
Closed
88
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103
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Manual
Priority
Created date
Last updated
Milestone due date
Due date
Popularity
Label priority
Manual
Title
Add option to perform diffex-test in mf_feat_counts.R using fc-cutoff > 0.
#12
· created
Apr 10, 2017
by
brandl
rna_seq
CLOSED
2
updated
Jun 19, 2017
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
export TPM instead of FPKM tables
#14
· created
May 19, 2017
by
brandl
rna_seq
CLOSED
1
updated
Jun 19, 2017
try RNA-SeQC to get qc for bam files
#15
· created
May 19, 2017
by
brandl
CLOSED
1
updated
Dec 09, 2019
auto-detect strandedness when extracting count matrix
#16
· created
May 29, 2017
by
brandl
CLOSED
2
updated
Mar 27, 2020
better handling of outliers
#17
· created
May 30, 2017
by
brandl
CLOSED
0
updated
Mar 07, 2019
impl better means to access summary and quality statististcs
#18
· created
May 30, 2017
by
brandl
CLOSED
0
updated
Nov 09, 2017
Export counts as TPM in featcounts_deseq_mf.R
#9
· created
May 18, 2016
by
brandl
rna_seq
CLOSED
0
updated
Jul 08, 2017
create tool to create igv session file list of bam files
#8
· created
May 14, 2016
by
brandl
rna_seq
CLOSED
1
updated
Jul 08, 2017
couldn't export the bitr function in clusterprofiler
#3
· created
Mar 08, 2016
by
lakshman
CLOSED
6
updated
Jul 08, 2017
error in the plotDispEsts()
#2
· created
Mar 07, 2016
by
lakshman
CLOSED
7
updated
Jul 08, 2017
make sure that exported tables contain double-normalized counts and not just size-normalized ones
#1
· created
Feb 05, 2016
by
brandl
rna_seq
CLOSED
2
updated
Feb 12, 2019
use common q-score color scale for enrichment plots in cp_enrichment.R
#19
· created
Jul 19, 2017
by
brandl
CLOSED
0
updated
Nov 09, 2017
Integrate tools to assess gc/3/5 bias, insert size, and capture efficiency
#11
· created
Oct 11, 2016
by
brandl
rna_seq
CLOSED
1
updated
Feb 20, 2020
use http://multiqc.info/ for qc reporting
#10
· created
Jul 29, 2016
by
brandl
rna_seq
CLOSED
1
updated
Nov 18, 2019
finish panther enrichment and reintegrate into cp_enrichment.R
#7
· created
May 12, 2016
by
brandl
rna_seq
CLOSED
2
updated
Feb 20, 2020
Add pcr duplication analysis for rna-seq workflow
#6
· created
Apr 22, 2016
by
brandl
rna_seq
CLOSED
0
updated
Nov 09, 2017
add frip statistic to cs-workflow
#5
· created
Mar 18, 2016
by
brandl
CLOSED
1
updated
Mar 07, 2019
Add groupGo to cp_enrichment
#4
· created
Mar 16, 2016
by
brandl
CLOSED
1
updated
Nov 09, 2017
write shiny app (results relative local app) for dge data
#22
· created
Nov 09, 2017
by
herseman
CLOSED
0
updated
Jan 19, 2018
consider to use alpha for more correct p_adjustment
#23
· created
Nov 14, 2017
by
brandl
CLOSED
5
updated
May 14, 2020
report improvements
#25
· created
Nov 16, 2017
by
brandl
CLOSED
1
updated
Feb 20, 2020
update to more recent https://github.com/deeptools/deepTools/releases
#26
· created
Aug 16, 2018
by
brandl
2h
CLOSED
3
updated
Feb 20, 2020
new ticket
#27
· created
Nov 15, 2018
by
brandl
3h
CLOSED
3
updated
Dec 07, 2018
ms_workflow: Improvemnts
7 of 9 tasks completed
#28
· created
Dec 07, 2018
by
brandl
mass_spec
CLOSED
3
updated
Dec 10, 2019
revise limma workflow for mass spec data
#29
· created
Jan 10, 2019
by
herseman
CLOSED
1
updated
Jan 11, 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
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: 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: 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
ms_workflow: handling of contaminations
#37
· created
Feb 08, 2019
by
herseman
mass_spec
CLOSED
1
updated
Dec 10, 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: 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
sc_workflow: update sc_quality_check.R
#42
· created
Feb 28, 2019
by
herseman
CLOSED
4
updated
Mar 20, 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
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
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
sc_workflow: add shinyApp to explore Seurat clusterings
#47
· created
Mar 20, 2019
by
herseman
CLOSED
5
updated
Mar 22, 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
general: think about using argparser instead of docopt for futur scripts
#52
· created
Jun 03, 2019
by
herseman
CLOSED
6
updated
May 26, 2020
general: Test packrat for keep reproducible R environments
#53
· created
Jun 04, 2019
by
domingue
CLOSED
4
updated
Sep 16, 2019
general: add multiQC report to fastqc_summary
#54
· created
Jun 05, 2019
by
herseman
CLOSED
4
updated
Dec 02, 2019
dge_workflow: include MA plot from ggpubr in dge report
#55
· created
Jun 07, 2019
by
herseman
CLOSED
1
updated
Jun 18, 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: error message because gtf_file did not exist
#58
· created
Jun 27, 2019
by
herseman
CLOSED
1
updated
Jun 27, 2019
MS worflow: improvements
#59
· created
Jul 17, 2019
by
domingue
CLOSED
10
updated
Aug 07, 2019
ms_workflow: add intensities to results table
#60
· created
Aug 09, 2019
by
domingue
mass_spec
CLOSED
2
updated
Aug 09, 2019
ms_workflow: add % of NAs to results table
#61
· created
Aug 09, 2019
by
domingue
mass_spec
CLOSED
1
updated
Aug 09, 2019
ms_workflow: replace PCA with plotly
#62
· created
Aug 09, 2019
by
domingue
mass_spec
CLOSED
2
updated
Aug 09, 2019
ms_workflow: add more explanations
#63
· created
Aug 09, 2019
by
domingue
mass_spec
CLOSED
1
updated
Aug 09, 2019
ms_workflow: QC improvments
#64
· created
Aug 09, 2019
by
domingue
mass_spec
CLOSED
1
updated
Aug 13, 2019
DEP installation on falcon - nc-config missing
#65
· created
Aug 14, 2019
by
domingue
mass_spec
CLOSED
1
updated
Sep 17, 2019
expression_explorer: harcoded Rscipt path
#67
· created
Aug 15, 2019
by
domingue
rna_seq
CLOSED
0
updated
Aug 21, 2019
ms_workflow: Add table with % of contaminants in the most abudant proteins
#68
· created
Aug 26, 2019
by
domingue
mass_spec
CLOSED
0
updated
Aug 26, 2019
ms_worflow: bug in heatmap clustering
#69
· created
Aug 27, 2019
by
domingue
mass_spec
CLOSED
1
updated
Aug 28, 2019
cut delimeter breaks fastqc_summary.R
#70
· created
Sep 09, 2019
by
domingue
rna_seq
CLOSED
0
updated
Sep 09, 2019
Grep error message crashes the script
#71
· created
Sep 09, 2019
by
domingue
rna_seq
CLOSED
0
updated
Sep 09, 2019
Changes in ggplot break boxplot in fastqc_summary.R
#72
· created
Sep 09, 2019
by
domingue
rna_seq
CLOSED
1
updated
Sep 09, 2019
Implement renvs
#73
· created
Sep 16, 2019
by
domingue
mass_spec
rna_seq
CLOSED
2
updated
Feb 20, 2020
dge_workflow: fix lcf help
#74
· created
Oct 22, 2019
by
domingue
rna_seq
CLOSED
0
updated
Dec 02, 2019
dge_workflow: future improvements
#75
· created
Oct 22, 2019
by
domingue
rna_seq
CLOSED
1
updated
Jul 20, 2020
iGenome permissions
#76
· created
Nov 15, 2019
by
domingue
rna_seq
CLOSED
0
updated
Feb 20, 2020
conda and bioconductor version
#77
· created
Jan 14, 2020
by
domingue
CLOSED
9
updated
Jan 21, 2020
Create stable conda enviroment for Single cell analysis conda on falcon
#78
· created
Jan 16, 2020
by
domingue
CLOSED
11
updated
Jul 08, 2020
updating ms_workflow
#79
· created
Jan 23, 2020
by
herseman
mass_spec
CLOSED
14
updated
Jul 13, 2020
MS: How is imputation done?
#80
· created
Jul 19, 2019
by
domingue
CLOSED
5
updated
Jan 24, 2020
dge _workflow: analyze duplicates has a broken link to the plot of the model (dupRadar)
#81
· created
Feb 10, 2020
by
domingue
rna_seq
CLOSED
1
updated
Feb 10, 2020
general: track unsynchronized files on the cluster
#82
· created
Feb 17, 2020
by
herseman
CLOSED
1
updated
Feb 17, 2020
ms_workflow: refine reorder information of protein groups
#83
· created
Feb 18, 2020
by
herseman
mass_spec
CLOSED
1
updated
Feb 18, 2020
dge_workflow: collect_kallisto_data.R fails for paired-end data
#84
· created
Mar 12, 2020
by
herseman
rna_seq
CLOSED
2
updated
Mar 12, 2020
Hardcoded pvalue in plot
#85
· created
Mar 13, 2020
by
domingue
rna_seq
CLOSED
5
updated
Apr 15, 2020
ms_workflow: ms_ms_prop and reorder information are missing for protein IDs without fasta_header information
#86
· created
Mar 17, 2020
by
herseman
mass_spec
CLOSED
1
updated
Mar 17, 2020
Move workflows to separate repositories
#87
· created
Mar 19, 2020
by
domingue
CLOSED
4
updated
Mar 20, 2020
general: create new human igenome for the Ensembl release 99
#89
· created
Jun 24, 2020
by
herseman
CLOSED
0
updated
Jun 24, 2020
argparser error when --bam_files is the last optional argument
#90
· created
Jul 01, 2020
by
domingue
rna_seq
CLOSED
4
updated
Jul 01, 2020
dge_workflow: expression_explorer app failed to load due to renamed/additional annotation columns
#91
· created
Jul 10, 2020
by
herseman
rna_seq
CLOSED
1
updated
Jul 10, 2020
GSEA
#92
· created
Aug 07, 2020
by
domingue
rna_seq
CLOSED
5
updated
Sep 23, 2020
GSEA: add option to use custom gene sets
#93
· created
Sep 09, 2020
by
domingue
rna_seq
CLOSED
1
updated
Sep 09, 2020
gsea: bug, hard-coded species
#94
· created
Sep 15, 2020
by
domingue
rna_seq
CLOSED
0
updated
Sep 15, 2020
gsea: bug, in extra sets the first line is being read as header
#95
· created
Sep 15, 2020
by
domingue
rna_seq
CLOSED
0
updated
Sep 15, 2020
gsea: generate results for each contrast
#96
· created
Sep 16, 2020
by
domingue
rna_seq
CLOSED
1
updated
Sep 23, 2020
Gene enrichment: script selects random genes if list too large
#98
· created
Oct 07, 2020
by
domingue
rna_seq
CLOSED
2
updated
Oct 07, 2020
gsea: better description
#99
· created
Nov 12, 2020
by
domingue
rna_seq
CLOSED
2
updated
Nov 19, 2020
exDesign: numeric vs categorical variables and shrinkage method
#100
· created
Feb 15, 2021
by
gohr
rna_seq
CLOSED
0
updated
Feb 23, 2021
GSEA: improve color code of KEGG pathways
#101
· created
Mar 23, 2021
by
gohr
rna_seq
CLOSED
0
updated
Mar 23, 2021
gsea: improvement of description
#102
· created
Apr 08, 2021
by
gohr
Bioinformatics
Internal
Non-rechargeable
rna_seq
CLOSED
1
updated
Apr 08, 2021
gsea: fixing expression explorer
#103
· created
Apr 08, 2021
by
gohr
Bioinformatics
Internal
Non-rechargeable
rna_seq
CLOSED
0
updated
Apr 08, 2021