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nanoporetech
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pipeline-transcriptome-de
Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads
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Snakefile AttributeError
#36
m-noonan
opened
1 year ago
1
convert workflow.included to list of strings
#35
dkoppstein
opened
1 year ago
1
SyntaxError: Input and output files have to be specified as strings or lists of strings
#34
correave
opened
2 years ago
1
syntax error: Input and output files have to be specified as strings or lists of strings.
#33
peterthorpe5
opened
2 years ago
3
mode(counts) %in% "numeric" is not TRUE issue when commenting strip_version does not work
#32
C-Pauli
opened
2 years ago
0
"Nothing to be done" when running locally
#31
nklier38
opened
3 years ago
1
Error with alignment to reference in gene_expression tutorial
#30
john-hancock
opened
3 years ago
0
DTU transcript.tsv contains adjusted p.values?
#29
callumparr
opened
3 years ago
0
salmon output --noLengthCorrection
#28
callumparr
opened
3 years ago
0
Error in dmDSdata
#27
xpli2020
opened
3 years ago
0
directional fix to the R code; env.yml and config with minor updates
#26
sagrudd
closed
3 years ago
1
trivial update
#25
sagrudd
closed
3 years ago
0
de_analysis error: "Error in `contrasts<-`(`*tmp*`, ..."
#24
hqs10
closed
3 years ago
1
What is different?
#23
peterkilfeather
closed
3 years ago
1
plot_dtu_res error
#22
rebeelouise
closed
3 years ago
2
Salmon version
#21
Dan-Lt
closed
3 years ago
1
Error in rule de_analysis: jobid: 9
#20
MustafaElshani
closed
3 years ago
4
bioconductor-genomeinfodbdata-1.2.3-r40_0
#19
MustafaElshani
closed
3 years ago
1
Error in pipeline
#18
charlottewright
closed
3 years ago
3
Inclusion of complete DEXSeq results in tabular output
#17
sagrudd
closed
3 years ago
0
Updates to snakemake and R4.0.x
#16
sagrudd
closed
4 years ago
0
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]])
#15
suvimake
closed
3 years ago
4
Error in running de_analysis script
#14
callumparr
closed
4 years ago
4
PDF file corrupted
#13
vgori
closed
4 years ago
1
Porblems with snakefile. WorkflowError in line 7.
#12
hqs10
closed
4 years ago
1
Snakemake fails
#11
hqs10
closed
4 years ago
1
counts are not gene
#10
sdwien
closed
4 years ago
1
conda version and snakemake incompatible?
#9
sdwien
closed
4 years ago
1
Question about input files
#8
weir12
closed
5 years ago
1
The pipeline was abruptly terminated in the first step
#7
weir12
closed
5 years ago
1
Running the pipeline with only two samples
#6
drc111
closed
5 years ago
1
Rule exception when running pipeline-transcriptome-de/scripts/R
#5
callumparr
closed
5 years ago
11
Fail at write.xlsx for raw salmon counts
#4
callumparr
closed
5 years ago
2
Similar but not identical Error in dmDSdata(counts = counts, samples = coldata) compare to #1:
#3
weir12
closed
5 years ago
5
A question about setting of config.yml
#2
weir12
closed
5 years ago
2
Error in dmDSdata(counts = counts, samples = coldata) :
#1
cerdelyan
closed
5 years ago
6