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scRNAseq: thoughts on merging datasets generating from different version of 10x cellranger?
scRNAseq Harmony 10x Seurat
updated 16 months ago by 6.9k • written 16 months ago by ▴ 130
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1.1k
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Integration with Harmony using seurat object + SCTransform
SCTransform seurat scRNAseq
23 months ago by simplitia ▴ 130
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1.1k
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Comment: Comment: How to tell if GEO SRA is paired or single?
2.0 years ago by simplitia ▴ 130
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4
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1.1k
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How to tell if GEO SRA is paired or single?
rnaseq geo
2.0 years ago by simplitia ▴ 130
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0
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1.1k
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Comment: Comment: How to tell if GEO SRA is paired or single?
2.0 years ago by simplitia ▴ 130
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1.0k
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Comment: Comment: How many IGH genes are there? Confused about nomenclature.
2.1 years ago by simplitia ▴ 130
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1.0k
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Comment: Comment: How many IGH genes are there? Confused about nomenclature.
2.1 years ago by simplitia ▴ 130
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1
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1.0k
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Comment: Comment: How many IGH genes are there? Confused about nomenclature.
2.1 years ago by simplitia ▴ 130
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6
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1.0k
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How many IGH genes are there? Confused about nomenclature.
rnaseq genecode
2.1 years ago by simplitia ▴ 130
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1
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2.6k
views
Comment: Comment: What are the units for the sctransform SCT scale.data slots?
2.3 years ago by simplitia ▴ 130
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1
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2.6k
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Comment: Comment: What are the units for the sctransform SCT scale.data slots?
2.3 years ago by simplitia ▴ 130
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5
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2.6k
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What are the units for the sctransform SCT scale.data slots?
10x Seurat scRNAseq
updated 2.3 years ago by 13k • written 2.3 years ago by ▴ 130
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29k
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Comment: Comment: Over Representation Vs Enrichment Analysis
2.4 years ago by simplitia ▴ 130
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0
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988
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Comment: Comment: For downstream analysis from cellranger 10x scRNAseq eg. Seurat package, do you
2.4 years ago by simplitia ▴ 130
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0
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4.9k
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Comment: Comment: What is the best practice of scRNA workflow for multiple patients and samples us
2.4 years ago by simplitia ▴ 130
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2
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988
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For downstream analysis from cellranger 10x scRNAseq eg. Seurat package, do you recommend using raw or filtered matrix?
10x Seurat scRNAseq
2.4 years ago by simplitia ▴ 130
4
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3
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1.1k
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Create a bed file bins from fasta?
bed fasta
updated 2.5 years ago by 13k • written 2.5 years ago by ▴ 130
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4
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954
views
Biologically what does it mean when an exon has higher expression?
expression rnaseq gene
updated 2.6 years ago by 13k • written 2.6 years ago by ▴ 130
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1
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954
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Comment: Comment: Biologically what does it mean when an exon has higher expression?
2.6 years ago by simplitia ▴ 130
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503
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Can RNAseq expression be correlated with differential methylated regions?
rnaseq methylation
2.9 years ago by simplitia ▴ 130
1
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1
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604
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What are the minimum packages required to compile samtools for Debian OS?
samtools
updated 2.9 years ago by ★ 28k • written 2.9 years ago by ▴ 130
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0
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1.9k
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Comment: Comment: Is there a way to safely remove all underscore from gene id for hg19 from geneco
2.9 years ago by simplitia ▴ 130
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1
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1.9k
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Comment: Comment: Is there a way to safely remove all underscore from gene id for hg19 from geneco
2.9 years ago by simplitia ▴ 130
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1
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1.9k
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Comment: Comment: Is there a way to safely remove all underscore from gene id for hg19 from geneco
2.9 years ago by simplitia ▴ 130
0
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1
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1.9k
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Comment: Comment: Is there a way to safely remove all underscore from gene id for hg19 from geneco
2.9 years ago by simplitia ▴ 130
0
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8
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1.9k
views
Is there a way to safely remove all underscore from gene id for hg19 from genecode
rnaseq genecode
2.9 years ago by simplitia ▴ 130
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0
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539
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Is there a Grange object for swiss-prot domain? What I want is to detect what domains are overlapping with genomic coordinates.
R
2.9 years ago by simplitia ▴ 130
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1
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733
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Anyone know what the window size ( bin size) for dmrcate is?
EPIC 450K methylation
updated 3.0 years ago by ★ 2.0k • written 3.0 years ago by ▴ 130
1
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0
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13k
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Comment: Comment: Automatic Outlier Detection for RNA-seq data
3.2 years ago by simplitia ▴ 130
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1
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13k
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Comment: Comment: Automatic Outlier Detection for RNA-seq data
3.2 years ago by simplitia ▴ 130
1
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0
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1.2k
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Comment: Comment: guilt by association
3.3 years ago by simplitia ▴ 130
1
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0
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3.8k
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Comment: Comment: Inserting Variant allele frequency to VCF file
3.3 years ago by simplitia ▴ 130
0
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0
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706
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Strelka2 stomatic calls, where is the GT tag ?
strelka annovar variant
3.3 years ago by simplitia ▴ 130
0
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1
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905
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converting genomic version for annovar database?
annovar variant
updated 3.3 years ago by ▴ 580 • written 3.3 years ago by ▴ 130
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0
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1.9k
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Comment: Comment: Is there a way to extract alignment score from STAR aligner bam files?
3.4 years ago by simplitia ▴ 130
7
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5
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1.9k
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Is there a way to extract alignment score from STAR aligner bam files?
rnaseq
3.4 years ago by simplitia ▴ 130
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0
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2.4k
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Answer: Answer: install R package
3.4 years ago by simplitia ▴ 130
0
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0
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35k
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Comment: Comment: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remov
3.6 years ago by simplitia ▴ 130
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1
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1.5k
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Comment: Comment: Extracting reads from fastq files with BBMAP?
3.6 years ago by simplitia ▴ 130
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3
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1.5k
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Extracting reads from fastq files with BBMAP?
bbmap fastq
updated 3.6 years ago by 147k • written 3.6 years ago by ▴ 130
0
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1
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35k
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Comment: Comment: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remov
3.6 years ago by simplitia ▴ 130
0
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1
reply
35k
views
Comment: Comment: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remov
3.6 years ago by simplitia ▴ 130
1
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1
reply
825
views
Convert COSMIC VCF coordinates to that of ensembl format?
sequencing SNP alignment next-gen
4.1 years ago by simplitia ▴ 130
0
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0
replies
800
views
Where can I get the GTex equivalent to rnaseqv2 Level3 RSEM_genes?
RNA-Seq tcga rsem
4.3 years ago by simplitia ▴ 130
0
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0
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29k
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Comment: C: How To Do Normalization Of Two Chip-Seq Data?
4.5 years ago by simplitia ▴ 130
0
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5
replies
2.7k
views
Calculating and confirming shRNA knockdown gene from RNA-Seq?
RNA-Seq
updated 4.5 years ago by ▴ 920 • written 7.1 years ago by ▴ 130
1
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1
reply
4.4k
views
Comment: C: How to round the "expected counts" to integers?
4.5 years ago by simplitia ▴ 130
1
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3
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1.5k
views
How reliable are the ensembl transcript isoforms?
RNA-Seq ensembl isoform
updated 4.6 years ago by ▴ 330 • written 4.6 years ago by ▴ 130
2
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1
reply
1.7k
views
GRanges: remove ranges that falls in between a larger range?
grange RNA-Seq r
updated 4.7 years ago by ▴ 40 • written 4.7 years ago by ▴ 130
0
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1
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9.4k
views
Comment: C: How to color nodes in Cytoscape according to expression of genes? How should the
4.8 years ago by simplitia ▴ 130
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