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Any alternatives to Cellranger aligner that Seurat can read?
scrna-seq rna-seq cellranger sequencing written 16 hours ago by louis-gil • 0 • updated 12 hours ago by ATpoint ♦ 40k
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30
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In Seurat, how do you decide the cutoff for nFeature_RNA?
scrna-seq R seurat written 2 days ago by jvbeltran0122 • 0
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43
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1
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Multi-group DE scRNA-seq comps without replicates
scrna-seq deseq2 seurat rna-seq written 2 days ago by LacquerHed • 0 • updated 2 days ago by khorms • 150
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84
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scRNA-seq, MONOCLE3, and trajectory reconstruction, and Moran I statistics
scrna-seq written 6 days ago by Bogdan • 1.0k
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46
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1
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cellranger: min gene count and UMI/cell filter?
scrna-seq qc cellranger 10x genomics written 6 days ago by mcsimenc • 10 • updated 6 days ago by swbarnes2 ♦ 8.9k
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149
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Removal of mRNA contamination from scRNA-seq data using SoupX: How to proceed when "Extremely high contamination estimated"?
scrna-seq soupx rna-seq written 6 days ago by AA • 0
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718
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8 follow
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Forum: Feature Selection in 10X scRNA-seq data
scrna-seq forum pca software-error written 9 months ago by ATpoint ♦ 40k
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67
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1
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Computational Biology Programming Course/Book
scrna-seq course code programming written 7 days ago by rafaelsolersanblas • 20 • updated 7 days ago by jared.andrews07 ♦ 7.6k
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54
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Package for RNA-Protein Interaction Network
scrna-seq single-cell tutorial rna-seq written 10 days ago by jvbeltran0122 • 0
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71
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Wilcoxon test, t-test and negative binomial test for DEG of scRNA-Seq data
scrna-seq deg differential expression written 10 days ago by CY • 550
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68
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What format should a dataframe be in to use the AddMetaData function in Seurat?
scrna-seq R seurat rna-seq written 13 days ago by Pratik Mehta • 30
2
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1
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112
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1
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Tumour heterogeneity in scRNA-seq - cell-to-cell correlation
scrna-seq tumour heterogeneity correlation written 4 weeks ago by dccroucher • 20 • updated 29 days ago by pacome.pr • 50
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116
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cluster identification in seurat
scrna-seq R seurat written 4 weeks ago by roberts • 30 • updated 4 weeks ago by jared.andrews07 ♦ 7.6k
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154
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PHATE Clustering Error
scrna-seq seurat phate error single cell written 4 weeks ago by fouerghi20 • 10 • updated 4 weeks ago by genomax ♦ 91k
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2
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147
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5 follow
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I need help with Starsolo and scRNA-seq
scrna-seq starsolo star rna-seq written 5 weeks ago by rafaelsolersanblas • 20
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207
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Job: Postgraduate Student in Bioinformatics and Liver Cancer Genomics
liver cancer ctdna job scrna-seq ngs liquid biopsy written 6 weeks ago by waihungh • 20
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1
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110
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1
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Reusability for scRNA-seq microfluidic chips
scrna-seq microfluidic chip written 6 weeks ago by Diedes • 20
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192
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News: [Webinar] Using t-SNE for data analysis : An Introduction by Dr. Laurens van der Maaten (Inventor of t-SNE, Research Director at Facebook AI Research)
scrna-seq news webinar t-sne written 6 weeks ago by Jennifer Pham • 380
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6 follow
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How to embed known cell information into Seurat object? AddMetaData?
scrna-seq R next-gen seurat3 written 6 weeks ago by Pratik Mehta • 30 • updated 6 weeks ago by swbarnes2 ♦ 8.9k
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219
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1
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Barplot of genes deferentially expressed in a few clusters
scrna-seq gene de seurat barplot written 8 weeks ago by mvis1231 • 30 • updated 7 weeks ago by swbarnes2 ♦ 8.9k
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138
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1
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Quality Control After Alignment
scrna-seq quality control rna-seq hisat2 written 8 weeks ago by asumani • 60
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1
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173
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1
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How can I align single RNA seq(scRNAseq) data by using STAR or another aligner?
scrna-seq droptag rna-seq single cell seq-well written 7 weeks ago by dhkwnr95 • 0 • updated 7 weeks ago by Rob ♦ 4.5k
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9 follow
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Split fastq according to barcodes
scrna-seq fastq demultiplexing written 22 months ago by Houyu Zhang • 20 • updated 9 weeks ago by SV • 0
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1
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163
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1
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different between SCTransform and NormalizeData
scrna-seq R sctransform normalization written 10 weeks ago by re_raz • 0
2
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312
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How to avoid over-correction by using harmony or CCA to batch correction in scRNA-seq?
scrna-seq R batch correction seurat harmony written 11 weeks ago by Lukadon77 • 0
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2
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243
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2
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single cell RNA analysis
scrna-seq sctransform memory seurat written 3 months ago by re_raz • 0
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147
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scRNA-seq data at different time points
scrna-seq written 3 months ago by Bogdan • 1.0k • updated 11 weeks ago by Biostar ♦♦ 20
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168
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Memory Error when running `scrublet`
scrna-seq scrublet doublet written 12 weeks ago by Assa Yeroslaviz • 1.4k
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191
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Estimating hetero/homogeneity of scRNAseq clusters
scrna-seq R written 4 months ago by jrleary • 130 • updated 12 weeks ago by Biostar ♦♦ 20
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mitochondrial/ribosomal protein genes in scRNA-seq analysis
scrna-seq data processing rna-seq written 22 months ago by chipolino • 40 • updated 3 months ago by jared.andrews07 ♦ 7.6k
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