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kfuku52
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amalgkit
RNA-seq data amalgamation for a large-scale evolutionary transcriptomics
BSD 3-Clause "New" or "Revised" License
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SLURM dependency
#101
kfuku52
closed
2 years ago
14
nlog vs log2
#100
kfuku52
closed
1 year ago
5
/bin/sh: 1: bc: not found
#99
kfuku52
closed
1 year ago
2
ERROR: cannot convert float NaN to integer
#98
kfuku52
closed
2 years ago
0
KeyError: 'avg_len'
#97
kfuku52
closed
2 years ago
0
Exception: Empty value(s) of total_bases were detected in the metadata table.
#96
kfuku52
closed
2 years ago
1
Rcorrector support
#95
kfuku52
closed
1 year ago
1
Amalgkit Wiki overhaul
#94
Hego-CCTB
closed
1 year ago
7
"IndexError: list index out of range" during "parallel-fastq-dump" in getfastq
#93
Hego-CCTB
closed
2 years ago
2
pandas.errors.IntCastingNaNError: Cannot convert non-finite values (NA or inf) to integer
#92
kfuku52
closed
2 years ago
0
KeyError: 'lib_layout'
#91
kfuku52
closed
2 years ago
0
--batch and load_metadata() duplicate the 1st metadata.tsv entry
#90
Hego-CCTB
closed
2 years ago
4
amalgkit metadata for specific SRA-IDs
#89
Hego-CCTB
closed
2 years ago
4
pandas.errors.IntCastingNaNError: Cannot convert non-finite values (NA or inf) to integer
#88
kfuku52
closed
2 years ago
0
ValueError: unknown url type: ''
#87
kfuku52
closed
2 years ago
0
.tsv's have columns shifted by one in amalgkit output
#86
docxology
closed
2 years ago
3
Species.tau file has NAs
#85
docxology
closed
2 years ago
6
Warning message: "cor(tc, method = dist_method) : the standard deviation is zero"
#84
docxology
closed
2 years ago
14
HDF5 dependency in kallisto
#83
kfuku52
closed
2 years ago
6
AttributeError: 'Namespace' object has no attribute 'updated_metadata_dir'
#82
kfuku52
closed
1 year ago
10
The cstmm help message is not accurately described
#81
kfuku52
closed
1 year ago
3
amalgkit sanity does not recognize safely_removed flag for single-end RNA-seq
#80
kfuku52
closed
2 years ago
16
ValueError: cannot convert float NaN to integer
#79
kfuku52
closed
2 years ago
1
redundant codes in quant
#78
kfuku52
closed
1 year ago
5
quant is broken
#77
kfuku52
closed
2 years ago
0
fastq detection in getfastq
#76
kfuku52
closed
1 year ago
1
getfastq is broken in single-end samples
#75
kfuku52
closed
2 years ago
0
Invalid values in is_sampled and is_qualified
#74
kfuku52
closed
2 years ago
3
How does getfastq handle private fastq?
#73
kfuku52
closed
2 years ago
1
Index file detection in amalgkit sanity
#72
kfuku52
closed
1 year ago
6
relative fastq path in amalgkit integrate
#71
kfuku52
closed
2 years ago
2
lib_layout may not be considered appropriately in amalgkit integrate
#70
kfuku52
closed
2 years ago
2
amalgkit integrate is too slow
#69
kfuku52
closed
1 year ago
12
confusion matrix
#68
kfuku52
closed
2 years ago
4
Suggested annotation by Zooma
#67
kfuku52
closed
1 year ago
7
cstmm: run normal TMM if there is only one species
#66
kfuku52
closed
3 years ago
2
More informative cstmm normalization factor histogram
#65
kfuku52
closed
1 year ago
1
curate wiki
#64
kfuku52
closed
3 years ago
6
--one_outlier_per_iter does not work
#63
kfuku52
closed
3 years ago
16
Enhancing the outlier exclusion
#62
kfuku52
opened
3 years ago
1
Error in h(simpleError(msg, call))
#61
kfuku52
closed
3 years ago
7
More info from fastp stderr
#60
kfuku52
closed
1 year ago
1
urllib/wget download
#59
kfuku52
closed
1 year ago
6
mapping_rate is wrong
#58
kfuku52
closed
3 years ago
7
bug caused by single quotes in the metadata table
#57
kfuku52
closed
3 years ago
0
--one_outlier_per_iter default changed
#56
kfuku52
opened
3 years ago
3
Calls: get_mapping_rate -> [<- -> [<-.data.frame
#55
kfuku52
closed
3 years ago
0
supporting in-house fastq input
#54
kfuku52
closed
3 years ago
19
species directory name
#53
kfuku52
closed
3 years ago
1
curate plot overhaul with ggplot2
#52
kfuku52
closed
2 years ago
8
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