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GenomicRanges RleList

6 months ago story.benjamin ▴ 20

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Views IRanges GRanges RleList

updated 4.1 years ago by Mike Smith ★ 6.6k • written 4.1 years ago by Assa Yeroslaviz ★ 1.5k

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iranges s4vectors rle rlelist

7.3 years ago endrebak85 ▴ 40

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bug genomicranges granges rlelist coverage

updated 7.7 years ago by Hervé Pagès 16k • written 7.7 years ago by xiaotong.yao23 ▴ 10

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delayedarray rlelist rle

updated 8.0 years ago by Peter Hickey ▴ 760 • written 8.0 years ago by davide risso ▴ 980

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genomicranges biocgenerics rlelist genomicvars iranges

updated 8.1 years ago by Hervé Pagès 16k • written 8.1 years ago by Devin King ▴ 20

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rlelist ifelse

updated 8.8 years ago by theobroma22 ▴ 10 • written 8.8 years ago by maltethodberg ▴ 180

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Views genomicalignments IRangesList coverage RleList

updated 9.3 years ago by Hervé Pagès 16k • written 9.3 years ago by ccanchaya • 0

8 results • Page 1 of 1

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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k

Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…

Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0

Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…

Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20

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…

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A: Multi-level experiments in Limma

Answer: Should voomWithQualityWeights still be used when the sample-specific weights var

Answer: DESeq2 for candidate gene analysis

DESeq2 for candidate gene analysis

Answer: DESeq2 for candidate gene analysis

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