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comments
0
votes
0
replies
411
views
Integration with Harmony using seurat object + SCTransform
SCTransform
seurat
scRNAseq
5 months ago by
simplitia
▴ 120
0
votes
0
replies
499
views
Comment:
Comment: How to tell if GEO SRA is paired or single?
6 months ago by
simplitia
▴ 120
3
votes
4
replies
499
views
How to tell if GEO SRA is paired or single?
rnaseq
geo
6 months ago by
simplitia
▴ 120
0
votes
0
replies
499
views
Comment:
Comment: How to tell if GEO SRA is paired or single?
6 months ago by
simplitia
▴ 120
1
vote
0
replies
428
views
Comment:
Comment: How many IGH genes are there? Confused about nomenclature.
7 months ago by
simplitia
▴ 120
1
vote
1
reply
428
views
Comment:
Comment: How many IGH genes are there? Confused about nomenclature.
7 months ago by
simplitia
▴ 120
1
vote
1
reply
428
views
Comment:
Comment: How many IGH genes are there? Confused about nomenclature.
7 months ago by
simplitia
▴ 120
8
votes
6
replies
428
views
How many IGH genes are there? Confused about nomenclature.
rnaseq
genecode
7 months ago by
simplitia
▴ 120
0
votes
1
reply
1.2k
views
Comment:
Comment: What are the units for the sctransform SCT scale.data slots?
10 months ago by
simplitia
▴ 120
0
votes
1
reply
1.2k
views
Comment:
Comment: What are the units for the sctransform SCT scale.data slots?
10 months ago by
simplitia
▴ 120
0
votes
5
replies
1.2k
views
What are the units for the sctransform SCT scale.data slots?
10x
Seurat
scRNAseq
updated 10 months ago by
rpolicastro
12k • written 10 months ago by
simplitia
▴ 120
0
votes
0
replies
26k
views
Comment:
Comment: Over Representation Vs Enrichment Analysis
11 months ago by
simplitia
▴ 120
1
vote
0
replies
457
views
Comment:
Comment: For downstream analysis from cellranger 10x scRNAseq eg. Seurat package, do you
11 months ago by
simplitia
▴ 120
0
votes
0
replies
2.5k
views
Comment:
Comment: What is the best practice of scRNA workflow for multiple patients and samples us
11 months ago by
simplitia
▴ 120
1
vote
2
replies
457
views
For downstream analysis from cellranger 10x scRNAseq eg. Seurat package, do you recommend using raw or filtered matrix?
10x
Seurat
scRNAseq
11 months ago by
simplitia
▴ 120
3
votes
3
replies
550
views
Create a bed file bins from fasta?
bed
fasta
updated 12 months ago by
rpolicastro
12k • written 12 months ago by
simplitia
▴ 120
0
votes
4
replies
585
views
Biologically what does it mean when an exon has higher expression?
expression
rnaseq
gene
updated 13 months ago by
rpolicastro
12k • written 13 months ago by
simplitia
▴ 120
0
votes
1
reply
585
views
Comment:
Comment: Biologically what does it mean when an exon has higher expression?
13 months ago by
simplitia
▴ 120
0
votes
0
replies
326
views
Can RNAseq expression be correlated with differential methylated regions?
rnaseq
methylation
17 months ago by
simplitia
▴ 120
1
vote
1
reply
398
views
What are the minimum packages required to compile samtools for Debian OS?
samtools
updated 17 months ago by
Mensur Dlakic
★ 23k • written 17 months ago by
simplitia
▴ 120
0
votes
0
replies
1.2k
views
Comment:
Comment: Is there a way to safely remove all underscore from gene id for hg19 from geneco
17 months ago by
simplitia
▴ 120
0
votes
1
reply
1.2k
views
Comment:
Comment: Is there a way to safely remove all underscore from gene id for hg19 from geneco
17 months ago by
simplitia
▴ 120
0
votes
1
reply
1.2k
views
Comment:
Comment: Is there a way to safely remove all underscore from gene id for hg19 from geneco
17 months ago by
simplitia
▴ 120
0
votes
1
reply
1.2k
views
Comment:
Comment: Is there a way to safely remove all underscore from gene id for hg19 from geneco
17 months ago by
simplitia
▴ 120
0
votes
8
replies
1.2k
views
Is there a way to safely remove all underscore from gene id for hg19 from genecode
rnaseq
genecode
17 months ago by
simplitia
▴ 120
0
votes
0
replies
367
views
Is there a Grange object for swiss-prot domain? What I want is to detect what domains are overlapping with genomic coordinates.
R
17 months ago by
simplitia
▴ 120
0
votes
1
reply
452
views
Anyone know what the window size ( bin size) for dmrcate is?
EPIC
450K
methylation
updated 18 months ago by
Basti
★ 1.6k • written 18 months ago by
simplitia
▴ 120
1
vote
0
replies
10k
views
Comment:
Comment: Automatic Outlier Detection for RNA-seq data
20 months ago by
simplitia
▴ 120
0
votes
1
reply
10k
views
Comment:
Comment: Automatic Outlier Detection for RNA-seq data
20 months ago by
simplitia
▴ 120
1
vote
0
replies
707
views
Comment:
Comment: guilt by association
22 months ago by
simplitia
▴ 120
0
votes
0
replies
2.3k
views
Comment:
Comment: Inserting Variant allele frequency to VCF file
22 months ago by
simplitia
▴ 120
0
votes
0
replies
468
views
Strelka2 stomatic calls, where is the GT tag ?
strelka
annovar
variant
22 months ago by
simplitia
▴ 120
0
votes
1
reply
603
views
converting genomic version for annovar database?
annovar
variant
updated 22 months ago by
Jianyu
▴ 570 • written 22 months ago by
simplitia
▴ 120
0
votes
0
replies
1.0k
views
Comment:
Comment: Is there a way to extract alignment score from STAR aligner bam files?
23 months ago by
simplitia
▴ 120
7
votes
5
replies
1.0k
views
Is there a way to extract alignment score from STAR aligner bam files?
rnaseq
23 months ago by
simplitia
▴ 120
0
votes
0
replies
1.6k
views
Answer:
Answer: install R package
23 months ago by
simplitia
▴ 120
0
votes
0
replies
26k
views
Comment:
Comment: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remov
2.1 years ago by
simplitia
▴ 120
0
votes
1
reply
1.0k
views
Comment:
Comment: Extracting reads from fastq files with BBMAP?
2.1 years ago by
simplitia
▴ 120
0
votes
3
replies
1.0k
views
Extracting reads from fastq files with BBMAP?
bbmap
fastq
updated 2.1 years ago by
GenoMax
129k • written 2.1 years ago by
simplitia
▴ 120
0
votes
1
reply
26k
views
Comment:
Comment: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remov
2.1 years ago by
simplitia
▴ 120
0
votes
1
reply
26k
views
Comment:
Comment: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remov
2.1 years ago by
simplitia
▴ 120
1
vote
1
reply
553
views
Convert COSMIC VCF coordinates to that of ensembl format?
sequencing
SNP
alignment
next-gen
2.6 years ago by
simplitia
▴ 120
0
votes
0
replies
619
views
Where can I get the GTex equivalent to rnaseqv2 Level3 RSEM_genes?
RNA-Seq
tcga
rsem
2.9 years ago by
simplitia
▴ 120
0
votes
0
replies
25k
views
Comment:
C: How To Do Normalization Of Two Chip-Seq Data?
3.0 years ago by
simplitia
▴ 120
0
votes
5
replies
2.2k
views
Calculating and confirming shRNA knockdown gene from RNA-Seq?
RNA-Seq
updated 3.1 years ago by
rohitsatyam102
▴ 690 • written 5.6 years ago by
simplitia
▴ 120
1
vote
1
reply
3.0k
views
Comment:
C: How to round the "expected counts" to integers?
3.1 years ago by
simplitia
▴ 120
1
vote
3
replies
1.0k
views
How reliable are the ensembl transcript isoforms?
RNA-Seq
ensembl
isoform
updated 3.2 years ago by
Astrid_Ensembl
▴ 330 • written 3.2 years ago by
simplitia
▴ 120
2
votes
1
reply
1.4k
views
GRanges: remove ranges that falls in between a larger range?
grange
RNA-Seq
r
updated 3.2 years ago by
Strand NGS
▴ 40 • written 3.2 years ago by
simplitia
▴ 120
0
votes
1
reply
7.9k
views
Comment:
C: How to color nodes in Cytoscape according to expression of genes? How should the
3.3 years ago by
simplitia
▴ 120
0
votes
1
reply
14k
views
Answer:
A: TMM or TPM normalized counts for visualization?
3.6 years ago by
simplitia
▴ 120
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