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sterrettJD
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HoMi
Host-microbiome dual transcriptome pipeline
https://homi-pipeline.readthedocs.io
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Add taxa barplot for kraken
#79
sterrettJD
closed
1 week ago
0
Kraken taxa barplot
#78
sterrettJD
closed
1 week ago
1
Synthetic transcriptomes benchmarks
#77
sterrettJD
closed
1 week ago
0
Setup benchmarking against Pereira's mock communities
#76
sterrettJD
closed
3 weeks ago
0
Taxa barplot can't find pseq in prep_mdf
#75
sterrettJD
closed
1 month ago
2
Benchmarks may need new dockerfile
#74
sterrettJD
opened
1 month ago
0
Polyester simulations still don't give the correct number of total reads for small communities
#73
sterrettJD
closed
1 month ago
1
Benchmarks on mock communities
#72
sterrettJD
closed
1 week ago
3
Dependency version issues necessitate dockerization
#71
sterrettJD
opened
3 months ago
0
Better txome simulation + Humann/Metaphlan versioning + readcounter
#70
sterrettJD
closed
3 months ago
0
Metaphlan database compatibility
#69
sterrettJD
closed
3 months ago
1
Expand benchmarking and add read reports
#68
sterrettJD
closed
3 months ago
0
fix phyla grabber
#67
sterrettJD
closed
4 months ago
0
R packages
#66
sterrettJD
closed
4 months ago
0
multiple Rmd files try to install packages at the same time and can't do that
#65
sterrettJD
closed
4 months ago
1
humann can't find metaphlan db
#64
sterrettJD
closed
4 months ago
1
Fix r imports
#63
sterrettJD
closed
4 months ago
0
Some Rmd files will error if also downloading packages
#62
sterrettJD
closed
4 months ago
0
Breakdown counts of reads
#61
sterrettJD
closed
3 months ago
1
Extra rule args
#60
sterrettJD
closed
4 months ago
0
Nonpareil params should be more customizable
#59
sterrettJD
closed
4 months ago
1
Using a cluster profile no longer works with snakemake >8.0.0
#58
sterrettJD
opened
4 months ago
0
Start benchmarking setup on synthetic communities
#57
sterrettJD
closed
4 months ago
0
Fix some docs optics
#56
sterrettJD
closed
4 months ago
0
Add a config file checker
#55
sterrettJD
closed
6 months ago
0
Add hisat2 functionality
#54
sterrettJD
closed
6 months ago
0
No host samples works okay
#53
sterrettJD
closed
8 months ago
0
When host transcriptome is disabled for all samples, generate_feature_counts errors
#52
sterrettJD
closed
8 months ago
1
Add TPM
#51
sterrettJD
closed
9 months ago
0
Support other host transcriptome aligners
#50
sterrettJD
closed
6 months ago
2
remove input requirements from setup_profile
#49
sterrettJD
closed
9 months ago
0
Add alternative working directory functionality
#48
sterrettJD
closed
9 months ago
0
Readthedocs doesn't get the right path to figures in README.md
#47
sterrettJD
closed
4 months ago
1
Clean targets
#46
sterrettJD
closed
9 months ago
0
Start auto documentation
#45
sterrettJD
closed
9 months ago
0
Hyperthreadedness
#44
sterrettJD
closed
9 months ago
0
Allow option for non-hyperthreaded cluster
#43
sterrettJD
closed
9 months ago
1
Kraken db params
#42
sterrettJD
closed
10 months ago
0
Automatic documentation for rules
#41
sterrettJD
closed
9 months ago
1
Tests for slurm integration?
#40
sterrettJD
opened
10 months ago
0
Clean unneeded
#39
sterrettJD
closed
10 months ago
0
Generate TPM and deseq-normalized host read counts
#38
sterrettJD
closed
4 months ago
1
Slurm extra
#37
sterrettJD
closed
10 months ago
0
kraken bracken resources
#36
sterrettJD
closed
10 months ago
1
Github action for unit tests on push/pull request
#35
sterrettJD
closed
10 months ago
1
Add rule-specific slurm_extra from config file
#34
sterrettJD
closed
10 months ago
1
Add new name options for default partitions
#33
sterrettJD
closed
10 months ago
0
HoMi config should be sanitized
#32
sterrettJD
closed
6 months ago
1
Users can specify samples to not map against the host genome
#31
sterrettJD
closed
10 months ago
0
More tests!
#30
sterrettJD
opened
10 months ago
0
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