@dmitriisev @Sanbomics It depends on how gene-level analysis is done. Sleuth, e.g., uses p-value aggregation of txp-level results to perform gene-level differential analysis (https://t.co/FtAcbAq6G1), so the bootstraps will, of course, affect txp-level p-v
@jjmerkin @JamesPBLloyd @hjpimentel Sorry, broken link. This: https://t.co/ICztD0KnAc
RT @hjpimentel: @StefanoBerto83 @marcotrizzino Not quite true, definitely not true in the general case: https://t.co/AYJgJUKlF9
@StefanoBerto83 @marcotrizzino Not quite true, definitely not true in the general case: https://t.co/AYJgJUKlF9
@hrksrkr @alex_mawla @CSoneson @mikelove @sinabooeshaghi Which in turn was motivated by https://t.co/JOEI5a2Qbz
The report of "Yi et al. Genome Biology (2018) 19:53 (https://t.co/NvKwhLLLtt) gives a clear answer to this question. In short, the sleuth analysis with gene expression may be the good option after the kallisto process. (https://t.co/f5MTiSlmrU)
RT @biorxiv_pubd: Gene-level differential analysis at transcript-level resolution published as: https://t.co/Gh5pSKTNuM @GenomeBiology #bio…
Gene-level differential analysis at transcript-level resolution published as: https://t.co/Gh5pSKTNuM @GenomeBiology #biorxiv
See also https://t.co/z7A4hR4f3C (with @lynn__yi @hjpimentel @yarbsalocin) for an analogous approach that can be used for *bulk* RNA-seq
@tiberi_simone @AliciaOshlack @marekcmero @nadia_davidson Removing them is also the approach taken by @lynn__yi, @pmelsted and @lpachter in https://t.co/TfTstQSqBh Would be nice extension though.
@AliciaOshlack @marekcmero @nadia_davidson How does this compare to https://t.co/FKlbabOSCL which also tests differential EC counts (aka TCC)?
RT @DGautheret: One knew it already but always good to be reminded that Gene level expression is best evaluated at transcript level... http…
One knew it already but always good to be reminded that Gene level expression is best evaluated at transcript level... https://t.co/WQXf0O9Gdo
RT @GenomeBiology: @GenomeBiology Linn Yi, @hjpimentel, @yarbsalocin, @lpachter apply Lancaster method to aggregating transcripts for gene-…
Gene-level differential analysis at transcript-level resolution https://t.co/qqhJK0cLOE
"Gene-level differential analysis at transcript-level resolution." Lynn Yi, Harold Pimentel, Nicolas L. Bray and Lior Pachter Genome Biology 2018; 19:53 https://t.co/WLpK4XZuXT
RT @TheMarcelSchulz: Gene-level differential analysis at transcript-level resolution https://t.co/NcD3TEDuwY #RNAseq
RT @TheMarcelSchulz: Gene-level differential analysis at transcript-level resolution https://t.co/NcD3TEDuwY #RNAseq
RT @TheMarcelSchulz: Gene-level differential analysis at transcript-level resolution https://t.co/NcD3TEDuwY #RNAseq
Gene-level differential analysis at transcript-level resolution https://t.co/NcD3TEDuwY #RNAseq
RT @GenomeBiology: @GenomeBiology Linn Yi, @hjpimentel, @yarbsalocin, @lpachter apply Lancaster method to aggregating transcripts for gene-…
Gene-level differential analysis at transcript-level resolution https://t.co/90QkGkkzuF #RNAseq #bioinformatics via @GenomeBiology @lpachter
Gene-level differential analysis at transcript-level resolution https://t.co/ayQFry4xw0
Gene-level differential analysis at transcript-level resolution https://t.co/CsCICCltwN
RT @GenomeBiology: @GenomeBiology Linn Yi, @hjpimentel, @yarbsalocin, @lpachter apply Lancaster method to aggregating transcripts for gene-…
RT @GenomeBiology: @GenomeBiology Linn Yi, @hjpimentel, @yarbsalocin, @lpachter apply Lancaster method to aggregating transcripts for gene-…
Gene-level differential analysis at transcript-level resolution https://t.co/aOJFEVPRf8
Gene-level differential analysis at transcript-level resolution https://t.co/ZUTThHIVkI
RT @nextgenseek: Gene-level differential analysis at transcript-level resolution from @lpachter group https://t.co/4E1mDdiELL https://t.co…
RT @nextgenseek: Gene-level differential analysis at transcript-level resolution from @lpachter group https://t.co/4E1mDdiELL https://t.co…
Gene-level differential analysis at transcript-level resolution from @lpachter group https://t.co/4E1mDdiELL https://t.co/jQ2qNEjh99
Gene-level differential analysis at transcript-level resolution https://t.co/T2z3W707FN
RT @GenomeBiology: @GenomeBiology Linn Yi, @hjpimentel, @yarbsalocin, @lpachter apply Lancaster method to aggregating transcripts for gene-…
RT @GenomeBiology: @GenomeBiology Linn Yi, @hjpimentel, @yarbsalocin, @lpachter apply Lancaster method to aggregating transcripts for gene-…
RT @GenomeBiology: @GenomeBiology Linn Yi, @hjpimentel, @yarbsalocin, @lpachter apply Lancaster method to aggregating transcripts for gene-…
RT @yarbsalocin: Congrats to @lynn__yi for her excellent work here! https://t.co/vF4lwbMy83
A method developed by @hjpimentel, @yarbsalocin, @lpachter can be applied to transcript compatibility counts obtained from pseudoalignment of reads, which circumvents the need for quantification and is fast, accurate, and model-free. Check it out at https:
It's out! https://t.co/f0HJgZacn0
RT @GenomeBiology: @GenomeBiology Linn Yi, @hjpimentel, @yarbsalocin, @lpachter apply Lancaster method to aggregating transcripts for gene-…
RT @GenomeBiology: @GenomeBiology Linn Yi, @hjpimentel, @yarbsalocin, @lpachter apply Lancaster method to aggregating transcripts for gene-…
RT @GenomeBiology: @GenomeBiology Linn Yi, @hjpimentel, @yarbsalocin, @lpachter apply Lancaster method to aggregating transcripts for gene-…
RT @yarbsalocin: Congrats to @lynn__yi for her excellent work here! https://t.co/vF4lwbMy83
RT @yarbsalocin: Congrats to @lynn__yi for her excellent work here! https://t.co/vF4lwbMy83
Congrats to @lynn__yi for her excellent work here! https://t.co/vF4lwbMy83
RT @GenomeBiology: @GenomeBiology Linn Yi, @hjpimentel, @yarbsalocin, @lpachter apply Lancaster method to aggregating transcripts for gene-…
RT @GenomeBiology: @GenomeBiology Linn Yi, @hjpimentel, @yarbsalocin, @lpachter apply Lancaster method to aggregating transcripts for gene-…
RT @GenomeBiology: @GenomeBiology Linn Yi, @hjpimentel, @yarbsalocin, @lpachter apply Lancaster method to aggregating transcripts for gene-…
RT @GenomeBiology: @GenomeBiology Linn Yi, @hjpimentel, @yarbsalocin, @lpachter apply Lancaster method to aggregating transcripts for gene-…
@GenomeBiology Linn Yi, @hjpimentel, @yarbsalocin, @lpachter apply Lancaster method to aggregating transcripts for gene-level differential analysis https://t.co/B8FIu1obaf