Showing : bayespeak • reset
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[bug] BayesPeak cannot deal with RangedData input
BayesPeak bug
9.2 years ago balwierz ▴ 40
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Error in bayespeak function importing data
bayespeak
10.2 years ago Reed ▴ 10
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ChIPseq-style peak calling for paired-end sequencing?
Chipseq DNAseq ATAC bayespeak narrowpeaks
updated 10.4 years ago by 53k • written 10.4 years ago by ▴ 140
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chip-seq data
ChIPSeq chipseq BayesPeak ChIPSeq chipseq BayesPeak
13.1 years ago John linux-user ▴ 210
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Question about ChIPpeakAnno R package
AnnotationData annotate ChIPpeakAnno BayesPeak AnnotationData annotate ChIPpeakAnno
13.2 years ago Julie Zhu ★ 4.3k
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Upgrade bioconductor to version 2.6
BayesPeak BayesPeak
14.1 years ago Mary Ellen Fitzpatrick ▴ 20
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error in bayespeak function
ChIPSeq GO BSgenome BSgenome chipseq BayesPeak ChIPSeq GO BSgenome BSgenome chipseq
updated 14.3 years ago by ▴ 130 • written 14.3 years ago by ▴ 810
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BayesPeak and RangedData obj output
BayesPeak BayesPeak
updated 15.0 years ago by ▴ 130 • written 15.0 years ago by ▴ 30
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BayesPeak segfault woes
BayesPeak BayesPeak
updated 15.4 years ago by ▴ 130 • written 15.4 years ago by ▴ 270
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Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 10
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
That's weird. Using the example data works for me. ``` > example(read10xCounts) rd10xC> # Mocking up some 10X genomics output. rd10xC> ex…
Comment: Join BOC Sciences at Drug Discovery Chemistry by teamardigen • 0
Sounds like an exciting event for anyone passionate about small molecule innovation. The focus on discovery and optimization really drives …
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Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Join BOC Sciences at Drug Discovery Chemistry
Drug datasets for RNA-seq
Comment: Check removeBatchEffect effectiveness
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