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PacMAN-pipeline
Bioinformatics pipeline for the analysis of amplicon sequencing data of eDNA samples from the PacMAN project
MIT License
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phyloseq object does not work with psadd::plot_krona
#104
pieterprovoost
opened
2 days ago
0
Use UDB database for vsearch
#103
pieterprovoost
opened
6 days ago
0
Remove special characters before taxon matching
#102
pieterprovoost
opened
1 week ago
0
Docker: configure strict channel priorities
#101
pieterprovoost
opened
1 week ago
0
Dockerfile and example config
#100
pieterprovoost
closed
1 week ago
0
Structured annotations and new WoRMS matching strategy
#99
pieterprovoost
closed
3 months ago
0
Add BLAST only detections
#98
pieterprovoost
closed
3 months ago
0
Missing RDP and VSEARCH sections in example config
#97
pieterprovoost
closed
1 week ago
0
sampleSizeValue does not appear to match sum of reads per ASV
#96
pieterprovoost
opened
4 months ago
0
Create cleanup script
#95
pieterprovoost
opened
5 months ago
0
make_dwca: argument is of length zero
#94
pieterprovoost
closed
10 months ago
0
dada2_ASV: Tibble columns must have compatible sizes.
#93
pieterprovoost
closed
10 months ago
1
Ensure that original identification is preserved regardless of WoRMS match
#92
pieterprovoost
opened
11 months ago
0
Add citation
#91
pieterprovoost
opened
11 months ago
0
Incorrect assignments in Everglades 12S
#90
pieterprovoost
closed
11 months ago
1
Improve occurrenceID naming
#89
pieterprovoost
opened
12 months ago
0
Fixes to taxonomy parsing in get-lsids
#88
pieterprovoost
closed
12 months ago
0
High level RDP classification despite good BLAST hits
#87
pieterprovoost
opened
12 months ago
0
Handle taxonomy strings from BLAST
#86
pieterprovoost
opened
12 months ago
0
Some DNADerivedData fields not exported
#85
pieterprovoost
opened
12 months ago
0
Dada2_ASVInference_Single: object 'abundance' not found
#84
pieterprovoost
opened
1 year ago
0
Write tests for taxonomic annotation
#83
pieterprovoost
opened
1 year ago
0
Vsearch hits and identities not properly included in compare_taxa
#82
pieterprovoost
closed
1 year ago
1
BLCA does not handle nan in taxonomy
#81
pieterprovoost
closed
1 year ago
0
Detect prefixed taxonomy strings
#80
pieterprovoost
closed
1 year ago
0
Add taxonomy confidence levels to DwC
#79
pieterprovoost
closed
1 year ago
1
Fix for missing votes in BLCA
#78
pieterprovoost
closed
1 year ago
0
BLCA: ValueError: max() arg is an empty sequence
#77
pieterprovoost
closed
1 year ago
0
Rename blca_identity_cutoff
#76
pieterprovoost
closed
1 year ago
1
Taxon matching improvements
#75
pieterprovoost
closed
1 year ago
0
Make results path configurable
#74
pieterprovoost
opened
1 year ago
0
Taxon matching stops silently with (429) Too Many Requests
#73
pieterprovoost
opened
1 year ago
1
Add clean taxonomy and scientific name
#72
pieterprovoost
closed
1 year ago
0
Incomplete taxon matching
#71
pieterprovoost
opened
1 year ago
0
Remove nan values from occurrence table
#70
pieterprovoost
opened
1 year ago
0
Change DwC-A file extensions to tsv or txt
#69
pieterprovoost
closed
1 year ago
0
AlignIO: No records found in handle
#68
pieterprovoost
closed
1 year ago
0
Sample IDs in report from sample metadata instead of manifest
#67
pieterprovoost
closed
1 year ago
0
Report fails due to absolute path for sample data
#66
pieterprovoost
closed
1 year ago
0
Add instructions for downloading NCBI nt
#65
pieterprovoost
opened
1 year ago
0
blastn: Out of memory
#64
pieterprovoost
opened
1 year ago
2
fix for no single reads after dada2 filtering
#63
SSuominen1
closed
1 year ago
0
Bugs
#62
SSuominen1
closed
1 year ago
0
Fix cutadapt finish all files before dada2
#61
SSuominen1
closed
1 year ago
1
dada2_filter: Error in files_exist[[i]]: subscript out of bounds
#60
pieterprovoost
closed
1 year ago
0
dada2_filter fails on missing unpaired cutadapt files
#59
pieterprovoost
closed
1 year ago
0
Incorrect taxonomy statistics in report
#58
pieterprovoost
opened
1 year ago
0
dada2_filter failing on missing cutadapt_unpaired output files
#57
pieterprovoost
closed
1 year ago
0
Report barcharts not readable in case of many samples
#56
pieterprovoost
opened
2 years ago
0
Bowtie2 and Cutadapt not available for Windows
#55
pieterprovoost
closed
2 years ago
1
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