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MPUSP
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nf-core-crispriscreen
Process next generation sequencing data obtained from CRISPRi repression library screenings
MIT License
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Consider adding bean counter as alternative fitness quantification tool
#35
m-jahn
opened
2 months ago
0
Consider adding chronos as alternative fitness quantification tool
#34
m-jahn
opened
2 months ago
0
feat: improved reporting, export of figures
#33
m-jahn
closed
5 months ago
1
feat: major update to modules, added singularity container, fixed plotting issues
#32
m-jahn
closed
5 months ago
1
update to nextflow 23 + module updates
#31
m-jahn
closed
5 months ago
0
Changed plotting options to fix problems which arose due to ggplot2 updates
#30
ute-hoffmann
closed
5 months ago
3
Exporting created images as .pdf, used data as .csv?
#29
ute-hoffmann
closed
5 months ago
15
count_summary.Rmd stalls at codechunk-10
#28
ute-hoffmann
closed
5 months ago
7
add singularity container for custom R env, required for DESeq and R markdown report modules
#27
m-jahn
closed
5 months ago
1
update contributors
#26
m-jahn
closed
1 year ago
0
Pipeline crashes when `gene_fitness = false` because it tries to generate fitness report
#25
m-jahn
closed
1 year ago
0
Fix fasta input without additional library
#24
ute-hoffmann
closed
1 year ago
2
Improve performance of Mageck MLE module
#23
m-jahn
closed
7 months ago
2
Mageck failing on big data sets
#22
ute-hoffmann
closed
1 year ago
4
If replicates were taken on different dates, calculation of correlation in calculate_fitness.R fails
#21
ute-hoffmann
closed
1 year ago
0
Add fitness report for `Mageck` output
#20
m-jahn
opened
1 year ago
7
Add CL parameter to pass a custom design matrix to Mageck
#19
m-jahn
closed
1 year ago
0
PCAs of samples? More QC measures?
#18
ute-hoffmann
closed
1 year ago
3
prepare_counts.R crashed due to wrong order of colnames
#17
ute-hoffmann
closed
1 year ago
1
MAPQ filtering after bowtie2 alignment
#16
ute-hoffmann
closed
1 year ago
1
add documentation for Mageck MLE
#15
m-jahn
closed
1 year ago
0
add `master` branch to github actions push trigger
#14
m-jahn
closed
1 year ago
0
Add alternative modules for fitness score calculation
#13
m-jahn
closed
1 year ago
2
include feature / parameter to remove known adapters from read sequence
#12
m-jahn
closed
1 year ago
1
Link in documentation broken
#11
ute-hoffmann
closed
1 year ago
3
Pipeline requires at least 10 CPUs
#10
ute-hoffmann
closed
1 year ago
3
nf-core module linting fails although `nf-core modules update` claims all is up to date
#9
m-jahn
closed
1 year ago
1
replace existing R containers with a version that is more complete
#8
m-jahn
closed
1 year ago
1
DESeq2 throws error when design is too simple
#7
m-jahn
closed
2 years ago
0
Add all options for running pipeline to `usage.md`
#6
m-jahn
closed
2 years ago
0
Consistent handling of time points in fitness calculation
#5
m-jahn
closed
2 years ago
2
Add final html report from Rmarkdown docoument with basic statistics and plots
#4
m-jahn
closed
2 years ago
1
Test behavior with A) paired end reads and B) incomplete/basic sample sheet
#3
m-jahn
opened
2 years ago
0
Add module to optionall reduce/downsample fastq files
#2
m-jahn
closed
2 years ago
1
Add quality trimming step e.g. using trim galore
#1
m-jahn
closed
2 years ago
1