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questions
1
vote
2
replies
441
views
RNA-seq differential expression across multiple tissues, 2 trials, and 2 conditions
RNA-seq
DESeq
EdgeR
Batch-effect
DEGs
10 days ago by
BioinfGuru
★ 1.6k
1
vote
2
replies
245
views
What GC content should I expect?
RNA-seq
GC-content
updated 11 days ago by
ATpoint
81k • written 12 days ago by
BioinfGuru
★ 1.6k
3
votes
2
replies
300
views
How do I collapse rows of a tibble in R?
R
tidyverse
tibble
collapse
18 days ago by
BioinfGuru
★ 1.6k
3
votes
2
replies
572
views
RNA-seq - Creating SAF from NCBI gff for Subread featureCounts - keep 'gene' or 'exon'
featureCounts
NCBI
Ensembl
GFF
rnaseq
updated 25 days ago by
Gordon Smyth
★ 6.9k • written 5 weeks ago by
BioinfGuru
★ 1.6k
3
votes
2
replies
2.4k
views
From cuffmerge to cuffdiff: What input for cuffdiff?
rna-seq
cuffmerge
cuffdiff
treated
controls
updated 3.5 years ago by
Biostar
20 • written 7.7 years ago by
BioinfGuru
★ 1.6k
3
votes
7
replies
2.3k
views
Tissue Specificity R-package
tissue specificity
R package
pipeline
publication
updated 4.7 years ago by
Biostar
20 • written 6.1 years ago by
BioinfGuru
★ 1.6k
8
votes
3
replies
4.7k
views
Confused about merging RNA-seq lanes/runs
Merge
RNA-seq
samples
runs
lanes
updated 5.8 years ago by
GenoMax
140k • written 5.8 years ago by
BioinfGuru
★ 1.6k
9
votes
7
replies
1.9k
views
Is the sequence quality good enough?
WGS
HISEQ4000
QC
5.8 years ago by
BioinfGuru
★ 1.6k
0
votes
0
replies
1.6k
views
Variant analysis on 1 or 2 samples: are the final steps of the GATK pipeline unneccessary?
SNP
GATK
pipeline
variant analysis
5.8 years ago by
BioinfGuru
★ 1.6k
2
votes
2
replies
2.4k
views
HaplotypeCaller output - All records are non-variant - Have I gone wrong somewhere?
SNP
haplotypecaller
NON_REF
gatk
5.8 years ago by
BioinfGuru
★ 1.6k
4
votes
12
replies
2.2k
views
Variant calling on single sample Macaque WGS data - advice please
Variant calling
mutect2
haplotypecaller
PON
5.8 years ago by
BioinfGuru
★ 1.6k
0
votes
3
replies
2.1k
views
MEME result v FIMO result for target annotation
meme
fimo
annotation
6.2 years ago by
BioinfGuru
★ 1.6k
6
votes
10
replies
3.6k
views
Can anyone suggest a RShiny app for displaying RNA-seq results online
rna-seq
rshiny
updated 6.3 years ago by
Charles Plessy
★ 2.9k • written 7.7 years ago by
BioinfGuru
★ 1.6k
6
votes
8
replies
1.9k
views
Is validation necessary?
pipeline
publications
validation
updated 10 months ago by
Ram
43k • written 6.4 years ago by
BioinfGuru
★ 1.6k
2
votes
3
replies
2.6k
views
Gene synonyms/aliases - Is there a way to collect them programmatically
gene
synonyms
alias
6.4 years ago by
BioinfGuru
★ 1.6k
0
votes
1
reply
1.6k
views
Transmembrane domain protein structure
protein
structure
prediction
transmembrane
updated 6.4 years ago by
cdsouthan
★ 1.9k • written 6.4 years ago by
BioinfGuru
★ 1.6k
0
votes
0
replies
957
views
Comparing expression of undifferentiated cells using ENCODE - which data sets?
ENCODE
RNA-seq
6.8 years ago by
BioinfGuru
★ 1.6k
7
votes
7
replies
5.4k
views
Heatmap - with diagonally split tiles
heatmap
split
6.8 years ago by
BioinfGuru
★ 1.6k
1
vote
1
reply
3.7k
views
MACS2 - centering peaks
MACS2
ChIP-Seq
peaks
centering
6.8 years ago by
BioinfGuru
★ 1.6k
1
vote
3
replies
3.3k
views
Meme: What is the optimal sequence length?
meme
sequence
length
fasta
updated 6.8 years ago by
pythiest
• 0 • written 7.4 years ago by
BioinfGuru
★ 1.6k
1
vote
2
replies
1.5k
views
simoultaneous chromatin + transcriptional profiling
chromatin
transcription
assay
updated 6.8 years ago by
Chirag Parsania
★ 2.0k • written 6.8 years ago by
BioinfGuru
★ 1.6k
54
votes
17
replies
5.7k
views
8 follow
Is annotation of enhancers to nearest gene pointless?
enhancer
annotation
updated 10 months ago by
Ram
43k • written 6.9 years ago by
BioinfGuru
★ 1.6k
0
votes
2
replies
3.0k
views
How do I select top 100,000 non-overlapping peaks from MACS2 narrow peaks output?
ATAC
MACS2
overlapping
narrow
peaks
updated 6.9 years ago by
Biostar
20 • written 7.0 years ago by
BioinfGuru
★ 1.6k
0
votes
0
replies
1.9k
views
Can I run nucleoatac with a consensus peak file?
nucleoatac
ATAC
ATAC-seq
7.0 years ago by
BioinfGuru
★ 1.6k
1
vote
2
replies
2.6k
views
Nucleoatac - extending broadPeak regions
Nucleoatac
ATAC-seq
updated 7.0 years ago by
igor
13k • written 7.0 years ago by
BioinfGuru
★ 1.6k
0
votes
0
replies
974
views
Where can I find CHIP-seq data for the suprachiasmatic nucleus?
ChIP-Seq
suprachiasmatic nucleus
7.3 years ago by
BioinfGuru
★ 1.6k
5
votes
7
replies
5.6k
views
Quantile normalisation: raw rpkm or log2rpkm?
rnaseq
quantile
normalisation
updated 7.5 years ago by
Michael
54k • written 7.5 years ago by
BioinfGuru
★ 1.6k
0
votes
1
reply
3.2k
views
Should I get the mean of 2 log2 transformed RPKM values?
rnaseq
log2
rpkm
7.5 years ago by
BioinfGuru
★ 1.6k
2
votes
3
replies
2.0k
views
How do I identify tissue specific genes for 1 small part of the brain?
tissue specific genes
brain
7.5 years ago by
BioinfGuru
★ 1.6k
2
votes
5
replies
7.9k
views
RNA-seq RPKM significance cut off
RNA-seq
RPKM
cutoff
updated 7.6 years ago by
Amitm
★ 2.2k • written 7.6 years ago by
BioinfGuru
★ 1.6k
2
votes
8
replies
7.5k
views
Rshiny - How do I check if user input exists in my data set?
Rshiny
textInput
validate
need
Shinyapp
updated 7.7 years ago by
Jean-Karim Heriche
27k • written 7.7 years ago by
BioinfGuru
★ 1.6k
2
votes
4
replies
2.2k
views
CummeRbund: I can't create a dispersion plot - help please?
RNA-Seq
cummeRbund
dispersionPlot
cuffData class
7.7 years ago by
BioinfGuru
★ 1.6k
9
votes
6
replies
3.4k
views
What is the purpose of running Cufflinks without a reference annotation?
cufflinks
reference annotation
7.7 years ago by
BioinfGuru
★ 1.6k
1
vote
4
replies
2.5k
views
Cuffdiff not performing tss, cds, splicing, promoter or CDS tests
RNA-Seq
cuffdiff
7.7 years ago by
BioinfGuru
★ 1.6k
0
votes
1
reply
2.1k
views
From cuffmerge to cuffdiff: Which .gtf files should be merged if assession differential gene expression
rna-seq
cuffmerge
cuffdiff
DEG
7.7 years ago by
BioinfGuru
★ 1.6k
0
votes
4
replies
2.9k
views
Cuffmerge: error duplicate GFF ID
cuffmerge
duplicate
error
GFF ID
7.7 years ago by
BioinfGuru
★ 1.6k
3
votes
4
replies
2.8k
views
Using igenome to run a seq analysis with Tophat/Cofflinks.....but how do I add the ERCC sequences to the the reference transcriptome and reference ge…
RNA-Seq
Rna-seq analysis
tophat
ERCC
mapping
7.7 years ago by
BioinfGuru
★ 1.6k
37 results • Page
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