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comments
0
votes
0
replies
24k
views
Comment:
Comment: Over Representation Vs Enrichment Analysis
10 days ago by
simplitia
▴ 80
1
vote
0
replies
216
views
Comment:
Comment: For downstream analysis from cellranger 10x scRNAseq eg. Seurat package, do you
14 days ago by
simplitia
▴ 80
0
votes
0
replies
1.9k
views
Comment:
Comment: What is the best practice of scRNA workflow for multiple patients and samples us
14 days ago by
simplitia
▴ 80
1
vote
2
replies
216
views
For downstream analysis from cellranger 10x scRNAseq eg. Seurat package, do you recommend using raw or filtered matrix?
10x
Seurat
scRNAseq
14 days ago by
simplitia
▴ 80
3
votes
3
replies
251
views
Create a bed file bins from fasta?
bed
fasta
updated 20 days ago by
rpolicastro
8.8k • written 21 days ago by
simplitia
▴ 80
0
votes
4
replies
332
views
Biologically what does it mean when an exon has higher expression?
expression
rnaseq
gene
updated 8 weeks ago by
rpolicastro
8.8k • written 8 weeks ago by
simplitia
▴ 80
0
votes
1
reply
332
views
Comment:
Comment: Biologically what does it mean when an exon has higher expression?
8 weeks ago by
simplitia
▴ 80
0
votes
0
replies
233
views
Can RNAseq expression be correlated with differential methylated regions?
rnaseq
methylation
5 months ago by
simplitia
▴ 80
1
vote
1
reply
278
views
What are the minimum packages required to compile samtools for Debian OS?
samtools
updated 6 months ago by
Mensur Dlakic
★ 20k • written 6 months ago by
simplitia
▴ 80
0
votes
0
replies
877
views
Comment:
Comment: Is there a way to safely remove all underscore from gene id for hg19 from geneco
6 months ago by
simplitia
▴ 80
0
votes
1
reply
877
views
Comment:
Comment: Is there a way to safely remove all underscore from gene id for hg19 from geneco
6 months ago by
simplitia
▴ 80
0
votes
1
reply
877
views
Comment:
Comment: Is there a way to safely remove all underscore from gene id for hg19 from geneco
6 months ago by
simplitia
▴ 80
0
votes
1
reply
877
views
Comment:
Comment: Is there a way to safely remove all underscore from gene id for hg19 from geneco
6 months ago by
simplitia
▴ 80
0
votes
8
replies
877
views
Is there a way to safely remove all underscore from gene id for hg19 from genecode
rnaseq
genecode
6 months ago by
simplitia
▴ 80
0
votes
0
replies
252
views
Is there a Grange object for swiss-prot domain? What I want is to detect what domains are overlapping with genomic coordinates.
R
6 months ago by
simplitia
▴ 80
0
votes
1
reply
287
views
Anyone know what the window size ( bin size) for dmrcate is?
EPIC
450K
methylation
updated 6 months ago by
Basti
▴ 490 • written 6 months ago by
simplitia
▴ 80
1
vote
0
replies
8.3k
views
Comment:
Comment: Automatic Outlier Detection for RNA-seq data
9 months ago by
simplitia
▴ 80
0
votes
1
reply
8.3k
views
Comment:
Comment: Automatic Outlier Detection for RNA-seq data
9 months ago by
simplitia
▴ 80
1
vote
0
replies
527
views
Comment:
Comment: guilt by association
11 months ago by
simplitia
▴ 80
0
votes
0
replies
1.3k
views
Comment:
Comment: Inserting Variant allele frequency to VCF file
11 months ago by
simplitia
▴ 80
0
votes
0
replies
322
views
Strelka2 stomatic calls, where is the GT tag ?
strelka
annovar
variant
11 months ago by
simplitia
▴ 80
0
votes
1
reply
436
views
converting genomic version for annovar database?
annovar
variant
updated 11 months ago by
Jianyu
▴ 570 • written 11 months ago by
simplitia
▴ 80
0
votes
0
replies
646
views
Comment:
Comment: Is there a way to extract alignment score from STAR aligner bam files?
12 months ago by
simplitia
▴ 80
7
votes
5
replies
646
views
Is there a way to extract alignment score from STAR aligner bam files?
rnaseq
12 months ago by
simplitia
▴ 80
0
votes
0
replies
889
views
Answer:
Answer: install R package
12 months ago by
simplitia
▴ 80
0
votes
0
replies
22k
views
Comment:
Comment: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remov
13 months ago by
simplitia
▴ 80
0
votes
1
reply
725
views
Comment:
Comment: Extracting reads from fastq files with BBMAP?
13 months ago by
simplitia
▴ 80
0
votes
3
replies
725
views
Extracting reads from fastq files with BBMAP?
bbmap
fastq
updated 13 months ago by
GenoMax
117k • written 13 months ago by
simplitia
▴ 80
0
votes
1
reply
22k
views
Comment:
Comment: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remov
13 months ago by
simplitia
▴ 80
0
votes
1
reply
22k
views
Comment:
Comment: Introducing Clumpify: Create 30% Smaller, Faster Gzipped Fastq Files. And remov
14 months ago by
simplitia
▴ 80
1
vote
1
reply
371
views
Convert COSMIC VCF coordinates to that of ensembl format?
sequencing
SNP
alignment
next-gen
20 months ago by
simplitia
▴ 80
0
votes
0
replies
503
views
Where can I get the GTex equivalent to rnaseqv2 Level3 RSEM_genes?
RNA-Seq
tcga
rsem
23 months ago by
simplitia
▴ 80
0
votes
0
replies
24k
views
Comment:
C: How To Do Normalization Of Two Chip-Seq Data?
2.1 years ago by
simplitia
▴ 80
0
votes
5
replies
2.0k
views
Calculating and confirming shRNA knockdown gene from RNA-Seq?
RNA-Seq
updated 2.1 years ago by
rohitsatyam102
▴ 530 • written 4.7 years ago by
simplitia
▴ 80
1
vote
1
reply
2.1k
views
Comment:
C: How to round the "expected counts" to integers?
2.1 years ago by
simplitia
▴ 80
1
vote
3
replies
758
views
How reliable are the ensembl transcript isoforms?
RNA-Seq
ensembl
isoform
updated 2.2 years ago by
Astrid_Ensembl
▴ 330 • written 2.2 years ago by
simplitia
▴ 80
2
votes
1
reply
1.1k
views
GRanges: remove ranges that falls in between a larger range?
grange
RNA-Seq
r
updated 2.3 years ago by
Strand NGS
▴ 40 • written 2.3 years ago by
simplitia
▴ 80
0
votes
1
reply
6.9k
views
Comment:
C: How to color nodes in Cytoscape according to expression of genes? How should the
2.4 years ago by
simplitia
▴ 80
0
votes
1
reply
12k
views
Answer:
A: TMM or TPM normalized counts for visualization?
2.7 years ago by
simplitia
▴ 80
1
vote
2
replies
1.2k
views
STAR: Is it ok to align with an index created from genecode but count features from gtf from ensembl?
RNA-Seq
STAR
alignment
updated 2.7 years ago by
Kristoffer Vitting-Seerup
★ 3.9k • written 2.7 years ago by
simplitia
▴ 80
0
votes
0
replies
391
views
How to interpret exon reads from recount for version 2?
RNA-Seq
TCGA
2.9 years ago by
simplitia
▴ 80
0
votes
0
replies
1.9k
views
Answer:
A: SOAPfuse: problem in constructing database
3.0 years ago by
simplitia
▴ 80
0
votes
0
replies
709
views
Advice for gene overlap with direction between two sets.
R
chisquare
statistics
3.2 years ago by
simplitia
▴ 80
0
votes
1
reply
1.0k
views
Comment:
C: Understanding FANTOM5 CAGE fields
3.4 years ago by
simplitia
▴ 80
2
votes
3
replies
1.0k
views
Understanding FANTOM5 CAGE fields
RNA-Seq
transcription
tss
updated 3.4 years ago by
Kristoffer Vitting-Seerup
★ 3.9k • written 3.4 years ago by
simplitia
▴ 80
0
votes
1
reply
1.1k
views
Help convert GDC exploration url to API download?
gdc
mutation
portal
updated 3.4 years ago by
Biostar
20 • written 3.5 years ago by
simplitia
▴ 80
0
votes
0
replies
151k
views
Comment:
A: How to download raw sequence data from GEO/SRA
updated 3.4 years ago by
Ram
36k • written 4.4 years ago by
simplitia
▴ 80
0
votes
1
reply
90k
views
Comment:
C: from .BAM to .BAI using samtools
3.5 years ago by
simplitia
▴ 80
0
votes
0
replies
3.2k
views
Comment:
C: How to recreate FASTQ from BAM
3.6 years ago by
simplitia
▴ 80
2
votes
4
replies
3.2k
views
How to recreate FASTQ from BAM
RNA-Seq
BAM
sequencing
updated 3.6 years ago by
ctseto
▴ 310 • written 3.6 years ago by
simplitia
▴ 80
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