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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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curate_group -> sample_group
#151
kfuku52
closed
4 months ago
3
Duplication rate and insert size peak from the fastp json report
#150
kfuku52
opened
7 months ago
0
Metadata example command
#149
docxology
closed
8 months ago
3
cstmm - curate incompatibility
#148
kfuku52
closed
8 months ago
4
Output uncorrected tables without going through all of curate
#147
Hego-CCTB
closed
6 months ago
3
Error in if (child1_color == child2_color) { :
#146
kfuku52
closed
11 months ago
0
Code for rRNA rate
#145
kfuku52
opened
11 months ago
1
Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length
#144
kfuku52
closed
11 months ago
0
Obsoleting search_term_*.config
#143
kfuku52
closed
11 months ago
3
amalgkit curate --h
#142
docxology
closed
11 months ago
1
ValueError: No objects to concatenate
#141
kfuku52
closed
11 months ago
0
FutureWarning: The argument 'infer_datetime_format' is deprecated and will be removed in a future version.
#140
kfuku52
closed
1 year ago
1
Effect of negative value clipping in log(x+1) values
#139
kfuku52
closed
8 months ago
1
use seqkit instead of pigz to compress fastq
#138
kfuku52
closed
8 months ago
0
mapping rate and cstmm factor in the curate SV predictive power plot
#137
kfuku52
closed
1 year ago
1
merge plot
#136
kfuku52
closed
8 months ago
1
amalgkit getfastq on folder with already-processed samples is re-running
#135
docxology
closed
1 year ago
13
getfastq OSError: [Errno 5] Input/output error:
#134
docxology
closed
1 year ago
1
print('layout = {}; Deleting unpaired file: {}'.format(sra_stat['layout'], unpaired_file)) NameError: name 'unpaired_file' is not defined
#133
docxology
closed
1 year ago
3
is_unpaird_file --> is_unpaired_file?
#132
docxology
closed
1 year ago
1
fastq-dump.2.8.0 err: column not found while opening table within short read archive module
#131
docxology
closed
1 year ago
3
broken csca
#130
kfuku52
closed
1 year ago
1
Error in data.frame(curate_group = curate_group_u, curate_group_color = curate_group_color[1:length(curate_group_u)],
#129
kfuku52
closed
1 year ago
6
NameError: name 'work_dir' is not defined
#128
kfuku52
closed
1 year ago
3
FileNotFoundError
#127
kfuku52
closed
1 year ago
6
restructure and simplify `metadata`
#126
kfuku52
closed
1 year ago
2
PCA with missing data
#125
kfuku52
closed
1 year ago
1
species-wise curate subdirectories
#124
kfuku52
closed
1 year ago
0
BUSCO-based csca
#123
kfuku52
closed
1 year ago
1
cstmm: directly specifying --orthogroup_table instead of OrthoFinder directory with --ortho
#122
kfuku52
closed
1 year ago
1
sanity --updated_metadata_dir
#121
kfuku52
closed
1 year ago
2
removing unnecessary dependencies
#120
kfuku52
closed
1 year ago
3
clean up csca.R
#119
kfuku52
closed
1 year ago
4
Semantic versioning
#118
kfuku52
closed
1 year ago
1
Obsoleting short options
#117
kfuku52
closed
1 year ago
1
amalgkit config writing files out of place
#116
kfuku52
closed
1 year ago
5
pandas.errors.IntCastingNaNError: Cannot convert non-finite values (NA or inf) to integer
#115
kfuku52
closed
1 year ago
19
amalgkit integrate assigns wrong file paths
#114
kfuku52
closed
1 year ago
1
sys.stderr.write('ERROR: could not find fastq file(s) in:', output_dir_getfastq)
#113
kfuku52
closed
1 year ago
1
quant --id
#112
kfuku52
closed
1 year ago
2
getfastq download options
#111
kfuku52
closed
1 year ago
2
pandas.errors.IntCastingNaNError: Cannot convert non-finite values (NA or inf) to integer
#110
kfuku52
closed
1 year ago
1
--config_dir
#109
kfuku52
closed
1 year ago
1
Error when a config file is missing
#108
kfuku52
closed
1 year ago
5
No expression data found. Please make sure `amalgkit merge` or `amalgkit cstmm` ran correctly and you provided the correct directory path
#107
kfuku52
closed
1 year ago
0
pandas 1.5
#106
kfuku52
closed
1 year ago
14
pandas.errors.EmptyDataError: No columns to parse from file
#105
kfuku52
closed
1 year ago
0
amalgkit config
#104
kfuku52
closed
1 year ago
10
Obsoleting updated_metadata
#103
kfuku52
closed
1 year ago
14
amalgkit quant terminating without error
#102
Hego-CCTB
closed
2 years ago
8
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