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162

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kissplice SNP output and kissDE runtime

R kissde rna-seq snp kissplice written 22 days ago by erica • 10 • updated 22 days ago by clara.benoitp • 10

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323

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kissDE error during 'diffExpressedVariants' step: "Error in data.frame..."

R kissde snp kissplice written 5 months ago by TrentGenomics • 30

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278

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problem in installing kissDE

snp kissde written 5 months ago by majeedaasim • 20 • updated 5 months ago by Ram ♦ 14k

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370

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kissDE: How do I use diffExpressedVariants with some zero counts in my data?

R diffexpressedvariants rna-seq kissde written 11 months ago by Zoe • 0

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827

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Error in running "diffExpressedVariants" function in kissDE R package

kissplice snp kissde written 19 months ago by c.evang • 10 • updated 16 months ago by vincent.lacroix • 80

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553

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Error running KissDE

kissde kissplice written 18 months ago by c.evang • 10

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Recent Replies

C: Modifying fasta file based on vcf information by Eli Korvigo • 120
Since the documentation is very scarce, it's hard to infer that `FastaVariant` ignores indels. Yo...
A: Cell type assignment in single-cell RNAseq by dppb05 • 0
[Monocle][1] can do it to some extent, although it is not 100% automatic. The performance will de...
C: FeatureCounts fails to count fragments instead of reads by Wietje • 110
Yes, I only filtered for "listed first in the file", something like this: samtools view -h i...
C: How to divide a data set into training and testing data set in MATLAB using cros by aouichechaimaa • 90
@arta yes, I already checked that link but didn't get what i want. My data is a matrix of 359 row...
C: Modifying fasta file based on vcf information by Eli Korvigo • 120
This might be an old question, but these days you can basically install any version of Java in a ...
C: metanalysis in R by russhh • 3.2k
There's many questions related to this. For example, see [this][1] from yesterday [1]: https:...
C: FeatureCounts fails to count fragments instead of reads by JJ • 170
I would assume that it does actually only check the first X reads and not all of them - would ta...
C: FeatureCounts fails to count fragments instead of reads by ATpoint • 3.5k
Are the mate reads of these multimappers still in the BAM file?
C: How to divide a data set into training and testing data set in MATLAB using cros by arta • 380
Have you looked [this][1] ? Apart from that, do you have to use just MATLAB, you can find more h...
C: 6-bp deletions in RNA-seq data by nancy • 30
"In short, the peak in 6-bp deletions is due to repetitive elements in the genome, and a single g...
A: Reference Guided De Novo assembly of Contigs generated from Illumina PE Reads by jean.elbers • 160
Ragout (https://github.com/fenderglass/Ragout) is also another option.
C: FeatureCounts fails to count fragments instead of reads by Wietje • 110
Thank you for the link, that confirms part of my idea. I would however assume that featureCounts ...

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