Bioconductor Single cell sequencing

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cmdscale zinbwave scRNA-seq single cell sequencing RNA-seq

updated 3.4 years ago by davide risso ▴ 930 • written 3.5 years ago by Wagaa ▴ 10

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assayData() scRNA-seq single cell sequencing assayData Bioconductor

updated 3.5 years ago by Kevin Blighe 3.9k • written 3.5 years ago by Wagaa ▴ 10

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single cell sequencing multi-omics data mining and integration Job

4.4 years ago • updated 4.3 years ago Julie Zhu ★ 4.3k

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single cell sequencing RNA-Seq ChIP-Seq ATAC-Seq Job

4.4 years ago • updated 4.3 years ago Julie Zhu ★ 4.3k

4 results • Page 1 of 1

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Comment: DESeq: Error in DESeqDataSet(se, design = design, ignoreRank) : some values i by ATpoint ★ 3.6k

What is the output of below_zero <- apply(miRNA_counts < 0, 1, sum) > 0 miRNA_counts[below_zero,,drop=FALSE]

Comment: Problem loading HDF5Array in R 4.3.2 by Mike Smith ★ 6.2k

Based on the error message this looks like the "invalid permissions" are referring to something in memory rather than your file system. If…

Comment: Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and by Aastha Kapoor • 0

After several attempts the code has worked. I connected to a faster internet connection. set the timeout (1000000) and run the command. I …

Comment: DESeq2 estimateSizeFactors iterate takes too long by Karthik • 0

Hello, I agree with you, and we are in process of working with collaborators, but I wanted to get a general opinion on the data and get a …

Comment: It's possible to use clusterProfiler without an annotationDBI package by Guido Hooiveld ★ 3.8k

Code to show it works: > library(clusterProfiler) > > ## use provided 10 IDs, plus as last one add ID that has a GO annotati…

Votes

Comment: Ensembl down???

Answer: Limma/DESeq2 for unbalanced nested design (paired samples)

Result from GSEA for non-model organism not as expected

Comment: DESeq2 estimateSizeFactors iterate takes too long

Answer: DESeq2 estimateSizeFactors iterate takes too long

Awards • All

Scholar to Mike Smith ★ 6.2k

Scholar to Hervé Pagès 16k