Issues · bioinfo / ngs_tools

New issue

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
report proportion of multi-mappers in STAR report

#20 · created Nov 09, 2017 by herseman
- 0
updated Nov 16, 2017
run kallisto parallel to STAR

#21 · created Nov 09, 2017 by herseman
- 0
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
DESeq2 check current clustering method

#24 · created Nov 15, 2017 by herseman
- 0
updated Nov 29, 2018
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 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: aggregate protein isoforms data on gene level

#32 · created Jan 15, 2019 by herseman mass_spec
- 0
updated Feb 08, 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
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: 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
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
ms_workflow: handling of technical replicates

#40 · created Feb 13, 2019 by herseman mass_spec
- 2
updated Dec 09, 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
ms_workflow: move to peptide level

#45 · created Mar 07, 2019 by herseman
- 0
updated Dec 10, 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: 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
dge_workflow: report number of reads per gene

#51 · created May 31, 2019 by herseman
- 14
updated Jun 30, 2020
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: 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
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
ms_workflow: improve the results heatmap 2 of 3 tasks completed

#66 · created Aug 15, 2019 by domingue mass_spec
- 1
updated Aug 23, 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
Stranded counts

#88 · created Mar 27, 2020 by domingue rna_seq
- 5
updated Jul 13, 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
gsea: improvments 2 of 4 tasks completed

#97 · created Sep 24, 2020 by domingue rna_seq
- 0
updated Oct 13, 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