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BIMSBbioinfo
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pigx_scrnaseq
Pipeline for analysis of Dropseq single cell data
http://bioinformatics.mdc-berlin.de/pigx
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m4/ax_r_package.m4 is outdated
#59
rekado
opened
2 years ago
0
Use common runner template.
#58
rekado
closed
3 years ago
1
new version of star will break the pipeline
#57
frenkiboy
opened
3 years ago
0
convert_matrix_from_mtx_to_loom:102 - ValueError: Length mismatch: Expected axis has 3 elements, new values have 2 elements
#56
smoe
opened
4 years ago
0
Update requirements - added flexbar, jellyfish, Seurat
#55
smoe
closed
4 years ago
0
Added missing dependency 'argparser'
#54
smoe
closed
4 years ago
0
check for corresponding chromosome names in GTF and fasta
#53
frenkiboy
opened
4 years ago
0
Local pipeline install fails during convert_matrix_from_mtx_to_loom.py
#52
t-carroll
opened
4 years ago
3
loom2sce should be called only once
#51
frenkiboy
opened
4 years ago
0
STAR breaks mm Matrix format for Velocyto output
#50
frenkiboy
opened
4 years ago
0
Pipeline dies on sort bam step if tmp files exist
#49
frenkiboy
opened
4 years ago
0
r-argparse should be checked by configure.ac
#48
rekado
closed
4 years ago
0
Add whitelist option to the pipeline
#47
frenkiboy
opened
4 years ago
0
Major code refactoring
#46
frenkiboy
closed
3 years ago
1
environment.yml file missing for conda installation
#45
davisidarta
closed
4 years ago
1
Replace dropseqtools with STAR solo
#44
frenkiboy
closed
4 years ago
1
FastqToSAM complains if header contains barcode
#43
frenkiboy
opened
6 years ago
0
Add number of cells per experiment to the report
#42
frenkiboy
opened
6 years ago
0
Rename slots in single cell experiment to standardly used names
#41
frenkiboy
opened
6 years ago
0
fix combine replicates
#40
egeulgen
closed
6 years ago
0
Experiment class
#39
egeulgen
closed
6 years ago
0
check whether the genome is defined
#38
frenkiboy
opened
6 years ago
0
Settings parsing - more descriptive error messages
#37
frenkiboy
opened
6 years ago
0
Verbosely describe how to contribute
#36
frenkiboy
opened
6 years ago
0
add descriptions
#35
egeulgen
closed
6 years ago
1
Provide Seurat object as output
#34
frenkiboy
closed
6 years ago
3
check whether the output directory is writeable
#33
frenkiboy
opened
6 years ago
0
mapping with hisat2
#32
frenkiboy
closed
4 years ago
1
Automatic merging of technical replicates
#31
frenkiboy
closed
6 years ago
0
Enable counting of intronic reads
#30
frenkiboy
closed
4 years ago
1
make iSEE/singleCellTK package work nicely with sce object produced by the pipeline
#29
frenkiboy
opened
6 years ago
1
test pipeline with R3.5 and updated packages
#28
frenkiboy
opened
6 years ago
0
too little explanation in the report
#27
al2na
closed
6 years ago
3
add barcode error correction
#26
frenkiboy
opened
6 years ago
0
Java fails with old kernel.
#25
Blosberg
closed
6 years ago
2
Redirect noisy output to log file
#24
Blosberg
opened
6 years ago
0
--printshellcmds not working
#23
Blosberg
opened
6 years ago
0
Log file output not going through on SM jobs on the cluster
#22
Blosberg
opened
6 years ago
0
add mitochondrial RNA contamination estimation
#21
frenkiboy
opened
6 years ago
0
Develop indrops parser
#20
frenkiboy
opened
6 years ago
0
Cluster compatibility
#19
Blosberg
closed
6 years ago
0
Add important stuff
#18
frenkiboy
closed
6 years ago
0
Add output folder description
#17
frenkiboy
closed
6 years ago
1
Add report description
#16
frenkiboy
opened
6 years ago
0
implement iSEE as the final step of the app
#15
frenkiboy
opened
6 years ago
0
Refactorized Dropseq.sh into snakemake rules - NOT TESTED
#14
frenkiboy
closed
6 years ago
0
Read count statistic and run + Rscript
#13
frenkiboy
closed
6 years ago
0
java using tools use user set TEMPDIR variable
#12
frenkiboy
closed
6 years ago
0
try out loomR/loompy for matrix merging
#11
frenkiboy
closed
6 years ago
1
Set TEMPDIR and java TEMPDIR locations
#10
frenkiboy
closed
6 years ago
2
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