Bioconductor Gencode

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recount RNAseq gencode lncRNA gene annotation

updated 6.0 years ago by chris.wilks ▴ 70 • written 6.0 years ago by francesco.gandolfi ▴ 20

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7.3k

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biomart rsubread gencode

updated 6.4 years ago by James W. MacDonald 68k • written 6.4 years ago by YinCY ▴ 20

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2.3k

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bsgenome variant calling whole exome sequence gencode reference genome

updated 6.6 years ago by Hervé Pagès 16k • written 6.6 years ago by svlachavas ▴ 840

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2.0k

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deseq2 tximport org.mm.eg.db gencode

7.0 years ago pvd2107 ▴ 30

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3.9k

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AnnotationHub Gencode GFF3 FASTA News

9.6 years ago Sonali Arora ▴ 390

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Answer: Help with the code for "BiocNeighbors::generic_find_knn() function used by scran by Aaron Lun ★ 28k

It's calling C++ code, see the relevant function definitions on [GitHub](https://github.com/knncolle/BiocNeighbors/blob/master/src/generics…

Answer: DESeq2 by ATpoint ★ 4.8k

Time courses are often inevitable batches but you should have done the library prep at the same day, just extract RNA per day. If not then …

Comment: Package developing and interoperation with Bioconductor by slizchap • 0

Thank you so much for your answer. This was very useful, I will optimize my functions so they can handle SE objects.

Comment: Package developing and interoperation with Bioconductor by slizchap • 0

Thank you so much for your answer, very useful!

Comment: Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files by Mike Smith ★ 6.6k

Tricky to try and debug this without some example files to work with. Can you provide the output of `traceback()` called immediately after…

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Is it possible to speed up VariantAnnotation's rowRanges function when converting to a dataframe?

Answer: Is it possible to speed up VariantAnnotation's rowRanges function when convertin

Comment: ComBat with repeated measures

Answer: Package developing and interoperation with Bioconductor

Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?

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