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questions
6
votes
5
replies
18k
views
7 follow
How different is rlog transformation from vst transformation in DESeq2
DESeq2
count normalization
updated 9 months ago by
ATpoint
82k • written 5.7 years ago by
piyushjo
▴ 700
0
votes
0
replies
667
views
MACS2: broad and broad no-model output peaks are exactly the same. Is something wrong?
ChIP-seq
macs2
H3K27ac
23 months ago by
piyushjo
▴ 700
8
votes
3
replies
4.0k
views
How to make an intronic GTF for alignment
RNA-Seq
intronic-gtf
updated 11 months ago by
Ram
43k • written 4.1 years ago by
piyushjo
▴ 700
7
votes
3
replies
1.8k
views
Sequencing PHRED quality confusion
fastqc
illumina 1.5
illumina 1.9
updated 4.2 years ago by
Istvan Albert
100k • written 4.2 years ago by
piyushjo
▴ 700
1
vote
5
replies
1.2k
views
All sequenced reads in piared end sequencing don't have mate pairs?
HISAT2
paired end sequencing
updated 4.2 years ago by
h.mon
35k • written 4.2 years ago by
piyushjo
▴ 700
1
vote
2
replies
2.5k
views
Does StringTie need strand information if HISAT2 was run with strand-specific information
HISAT2
STRINGTIE
updated 4.3 years ago by
humeira.tayyab
▴ 20 • written 4.8 years ago by
piyushjo
▴ 700
4
votes
3
replies
2.5k
views
Are liger or Seurat CCA good strategies for multiple scRNA-seq data integration?
scRNA-seq
dataset integration
updated 5 months ago by
e.r.zakiev
▴ 210 • written 4.4 years ago by
piyushjo
▴ 700
4
votes
6
replies
6.5k
views
Single cell clutering after regressing out cell cycle effect using seurat
seurat
scRNA-seq
clustering
updated 6 months ago by
Haci
▴ 680 • written 4.7 years ago by
piyushjo
▴ 700
5
votes
7
replies
5.1k
views
scRNA-seq analysis of two data-sets
seurat
scRNA-seq
updated 4.7 years ago by
jared.andrews07
★ 16k • written 4.7 years ago by
piyushjo
▴ 700
3
votes
3
replies
4.1k
views
what is inverse normalized RNA-seq expression and how to do that?
normalization
RNA-Seq
5.2 years ago by
piyushjo
▴ 700
2
votes
8
replies
2.5k
views
Comparing stranded reads to unstranded reads
RNA-Seq
DE gene
strand information
updated 5.3 years ago by
johnsonnathant
▴ 120 • written 5.3 years ago by
piyushjo
▴ 700
4
votes
2
replies
3.0k
views
Tips for network prediction: WGCNA vs ARACNE (or MINET)
network inference
aracne
wgcna
updated 5.4 years ago by
fuyingxue
▴ 20 • written 5.7 years ago by
piyushjo
▴ 700
0
votes
9
replies
2.3k
views
RNA-strandness of single cell library prep methods
scRNA-seq
smarter-seq
nextera
fluidigm
updated 2.5 years ago by
Ram
43k • written 5.4 years ago by
piyushjo
▴ 700
1
vote
1
reply
1.7k
views
Need help understanding ARACNe-AP output
aracne
PPI network
5.4 years ago by
piyushjo
▴ 700
2
votes
4
replies
3.2k
views
Creating interaction network using cytoscape
cytoscape
PPI
Expression data
updated 5.4 years ago by
scooter
▴ 620 • written 5.4 years ago by
piyushjo
▴ 700
1
vote
5
replies
1.6k
views
Conservation between mouse and human genes: form ensembl gene id?
gene conservation
ensembl
5.6 years ago by
piyushjo
▴ 700
1
vote
1
reply
1.1k
views
How comprehensive is genode lncrna anotation for mouse?
gencode
lncrna
mouse
5.7 years ago by
piyushjo
▴ 700
2
votes
0
replies
1.5k
views
Advantage of making HISAT2 genome index with annotation file
hisat2
reference index
annotations
updated 5.7 years ago by
Ram
43k • written 5.7 years ago by
piyushjo
▴ 700
1
vote
9
replies
2.6k
views
FASTQ file: duplicated sequences and overall poor quality
fasqtc
trimming
trimgalore
5.7 years ago by
piyushjo
▴ 700
6
votes
4
replies
1.7k
views
Difference in FPKM values of lncRNA when using different annotation files
gencode
reference annotations
updated 5.8 years ago by
grant.hovhannisyan
★ 2.6k • written 5.8 years ago by
piyushjo
▴ 700
1
vote
4
replies
2.0k
views
Cytoscape network view problem: running out of memory
cytoscape
aracne
5.8 years ago by
piyushjo
▴ 700
2
votes
10
replies
4.0k
views
Hisat2 index building taking days even with 40 GB RAM
sequencing
hisat2
build
updated 5.9 years ago by
Biostar
20 • written 6.1 years ago by
piyushjo
▴ 700
1
vote
4
replies
2.5k
views
gffread conversion leaves gene_id
gffread
gff to gtf
6.0 years ago by
piyushjo
▴ 700
0
votes
2
replies
1.2k
views
Primary assembly or patches: what to choose for making index file?
genome
hisat2
index
6.1 years ago by
piyushjo
▴ 700
24 results • Page
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