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RasmussenLab
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phamb
Downstream processing of VAMB binning for Viral Elucidation
MIT License
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category of viruses identified by PHAMB ?
#61
ChaoXianSen
opened
7 months ago
0
Can PHAMB be used directly for Virome analysis (enrichment of viral particles followed by sequencing)
#60
1023011930
opened
7 months ago
2
interpret the results of RF model
#59
ChaoXianSen
opened
8 months ago
0
How to Run - not in parallel - quick and dirty
#58
SergeyBaikal
opened
8 months ago
1
VAE or AAE?
#57
yqy6611
closed
8 months ago
1
how to get the file 'clusters.tsv' ?
#56
ChaoXianSen
opened
10 months ago
0
'run_RF.py' operation problem
#55
ChaoXianSen
opened
10 months ago
1
Binning question, how to use vamb?
#54
ChaoXianSen
opened
10 months ago
7
The predicted 'viral' number in 'vambbins_RF_predictions.txt' is inconsistent with the actual number in 'vamb_bins.1.fna'?
#53
ChaoXianSen
opened
10 months ago
1
What are the criteria of RF model
#52
ChaoXianSen
closed
10 months ago
2
how to evaluate the bin-annotations?
#51
ChaoXianSen
opened
10 months ago
1
split_contigs.py produces empty files
#50
ChaoXianSen
closed
10 months ago
2
Can PHAMB output comparable performance on environmental metagenome compared to gut metagenome
#49
liangjinsong
closed
10 months ago
1
split_contigs.py produces empty files
#48
Sanrrone
closed
7 months ago
1
High number of bacterial genes in phamb assembled bins
#47
ShailNair
closed
10 months ago
3
Update shebang lines in phamb python scripts
#46
jmtsuji
closed
1 year ago
2
contig length
#45
Dorothydu12
closed
1 year ago
1
Dev
#44
joacjo
closed
1 year ago
0
Parsing deepvirfinder line 512, in _parse_dvf_row contig_name, length, score, pvalue = line[:-1].split()
#43
TomasaSbaffi
closed
1 year ago
2
Versioned release package for Phamb
#42
jayramr
closed
1 year ago
16
modified header names in PHAMB
#41
ShailNair
opened
2 years ago
4
Question about the workflow
#40
Nianzhen-GU
opened
2 years ago
0
Including micomplete Arch131 and/or VIBRANT annotations?
#39
kellifeeser
opened
2 years ago
1
set full path for RF_model; fix error when parse DVF predictions file
#38
alienzj
opened
2 years ago
0
Empty or outcommented file
#37
susheelbhanu
closed
2 years ago
1
Running Phamb without reads
#36
jjensen44
closed
2 years ago
1
Vcheck on predicted viral bins
#35
barbarashih
closed
1 year ago
4
Suggestion : add checkv step beforehand to remove complete genomes
#34
michoug
opened
2 years ago
2
Random Forest Feature Names
#33
carrgomoo
closed
2 years ago
1
Running vamb/phamb using only Vibrant contigs
#32
michoug
closed
2 years ago
3
How can I control the total number of threads used by phamb?
#31
ilnamkang
closed
2 years ago
1
Result assessment!
#30
Jiulong-Zhao
closed
2 years ago
9
Running Phamb on long reads polished with short reads
#29
emilyjunkins
closed
2 years ago
1
Adapt for more recent Python versions.
#28
joacjo
closed
2 years ago
0
Issues about the installation of dependence
#27
Jiulong-Zhao
closed
2 years ago
5
Error while running RF model
#26
bhimbbiswa
closed
2 years ago
5
Dev
#25
joacjo
closed
2 years ago
0
Dev
#24
joacjo
closed
2 years ago
0
Documentation and RF script
#23
joacjo
closed
2 years ago
0
Suggesting changes to dvf.yaml
#22
bhimbbiswa
closed
2 years ago
0
MAGs?
#21
enryH
closed
2 years ago
1
Dev
#20
joacjo
closed
2 years ago
0
Dev
#19
joacjo
closed
2 years ago
1
Dev
#18
joacjo
closed
3 years ago
0
deal with corrupted DVF files
#17
joacjo
closed
3 years ago
0
edit Snakefile
#16
joacjo
closed
3 years ago
0
improve docs
#15
joacjo
closed
3 years ago
0
improving workflow and documentation
#14
joacjo
closed
3 years ago
0
Dev
#13
joacjo
closed
3 years ago
0
documentation
#12
joacjo
closed
3 years ago
0
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