nanoporetech pipeline-transcriptome-de issues

nanoporetech / pipeline-transcriptome-de

Pipeline for differential gene expression (DGE) and differential transcript usage (DTU) analysis using long reads

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issues

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Newest Most commented Recently updated Oldest Least commented Least recently updated

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

nanoporetech / pipeline-transcriptome-de

issues

Snakefile AttributeError

convert workflow.included to list of strings

SyntaxError: Input and output files have to be specified as strings or lists of strings

syntax error: Input and output files have to be specified as strings or lists of strings.

mode(counts) %in% "numeric" is not TRUE issue when commenting strip_version does not work

"Nothing to be done" when running locally

Error with alignment to reference in gene_expression tutorial

DTU transcript.tsv contains adjusted p.values?

salmon output --noLengthCorrection

Error in dmDSdata

directional fix to the R code; env.yml and config with minor updates

trivial update

de_analysis error: "Error in `contrasts<-`(`tmp`, ..."

What is different?

plot_dtu_res error

Salmon version

Error in rule de_analysis: jobid: 9

bioconductor-genomeinfodbdata-1.2.3-r40_0

Error in pipeline

Inclusion of complete DEXSeq results in tabular output

Updates to snakemake and R4.0.x

Error in `contrasts<-`(`tmp`, value = contr.funs[1 + isOF[nn]])

Error in running de_analysis script

PDF file corrupted

Porblems with snakefile. WorkflowError in line 7.

Snakemake fails

counts are not gene

conda version and snakemake incompatible?

Question about input files

The pipeline was abruptly terminated in the first step

Running the pipeline with only two samples

Rule exception when running pipeline-transcriptome-de/scripts/R

Fail at write.xlsx for raw salmon counts

Similar but not identical Error in dmDSdata(counts = counts, samples = coldata) compare to #1:

A question about setting of config.yml

Error in dmDSdata(counts = counts, samples = coldata) :