Bioconductor StringTie

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5.7k

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ballgown stringtie

updated 7.1 years ago by linda.boshans • 0 • written 8.2 years ago by bhawley1991 ▴ 10

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4.3k

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prepDE STRINGTIE deseq2

updated 5.6 years ago by Michael Love 41k • written 5.6 years ago by Nancy ▴ 10

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3.5k

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deseq2 StringTie RNA-seq normalisation

updated 4.4 years ago by Michael Love 41k • written 4.4 years ago by JindrichK • 0

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2.5k

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ballgown biologicalreplicates technical replicates stringtie

updated 6.4 years ago by Alyssa Frazee ▴ 210 • written 7.1 years ago by linda.boshans • 0

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1.8k

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hisat2 stringtie ballgown RNAseq

6.2 years ago • updated 6.0 years ago Nancy ▴ 10

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1.8k

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ballgown stringtie

updated 7.8 years ago by Jeff Leek ▴ 650 • written 7.8 years ago by alva.james • 0

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1.7k

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featureCount rna-seq gene_id re_gene_id stringtie

updated 5.3 years ago by Wei Shi ★ 3.6k • written 5.3 years ago by IRAIA.MAIALEN • 0

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1.5k

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tximport stringtie

6.2 years ago • updated 6.0 years ago matrs ▴ 10

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1.4k

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ballgown StringTie galaxy rnaseq

updated 22 months ago by Kevin Blighe ★ 3.9k • written 3.7 years ago by lakshmi9c • 0

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1.4k

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ballgown stringtie voom limma differential gene expression rnaseq

updated 7.6 years ago by Alyssa Frazee ▴ 210 • written 7.6 years ago by jcalis ▴ 10

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1.4k

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stringtie illumina hisat2 ballgown

updated 6.4 years ago by k.vitting.seerup ▴ 120 • written 6.4 years ago by amy16 • 0

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1.3k

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Ballgown Stringtie DEG rnaseq

6.0 years ago vharshavardhanan • 0

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1.3k

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tximport stringtie RNA-seq analysis

updated 5.4 years ago by James W. MacDonald 65k • written 5.4 years ago by Mithil Gaikwad • 0

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1.3k

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isoform RNA-seq hisat2 stringtie ballgown

3.6 years ago ra711 • 0

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720

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DESeq2 TPM rawcounts StringTie

updated 20 months ago by Michael Love 41k • written 20 months ago by snijesh ▴ 20

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274

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stringtie IsoformSwitchAnalyzeR pfamAnalyzeR gtf

updated 5 months ago by James W. MacDonald 65k • written 5 months ago by sumitra.20 • 0

16 results • Page 1 of 1

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Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40

1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…

Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0

Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …

Answer: PCA plot suggestions by Michael Love 41k

For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…

Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10

Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…

Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k

Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…

Votes

Answer: Dominance Index for Shotgun Metagenomics Data

Answer: Math expression in shapeCustom legend in EnhancedVolcano

Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length

Comment: Deseq2. decontXcounts not integers. Useful alternative?

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)

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