Profile Posts Awards
Show
all questions tools blogs news tutorials forum answers comments
Showing : questions
5
votes
4
replies
674
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq EdgeR DEGs DESeq2
13 days ago by BioinfGuru ★ 1.7k
1
vote
2
replies
480
views
RNA-seq differential expression across multiple tissues, 2 trials, and 2 conditions
RNA-seq DESeq EdgeR Batch-effect DEGs
6 weeks ago by BioinfGuru ★ 1.7k
1
vote
2
replies
288
views
What GC content should I expect?
RNA-seq GC-content
updated 6 weeks ago by 82k • written 6 weeks ago by ★ 1.7k
3
votes
2
replies
351
views
How do I collapse rows of a tibble in R?
R tidyverse tibble collapse
7 weeks ago by BioinfGuru ★ 1.7k
3
votes
2
replies
657
views
RNA-seq - Creating SAF from NCBI gff for Subread featureCounts - keep 'gene' or 'exon'
featureCounts NCBI Ensembl GFF rnaseq
updated 8 weeks ago by ★ 7.1k • written 10 weeks ago by ★ 1.7k
3
votes
2
replies
2.4k
views
From cuffmerge to cuffdiff: What input for cuffdiff?
rna-seq cuffmerge cuffdiff treated controls
updated 3.6 years ago by 20 • written 7.8 years ago by ★ 1.7k
3
votes
7
replies
2.3k
views
Tissue Specificity R-package
tissue specificity R package pipeline publication
updated 4.8 years ago by 20 • written 6.2 years ago by ★ 1.7k
8
votes
3
replies
4.8k
views
Confused about merging RNA-seq lanes/runs
Merge RNA-seq samples runs lanes
updated 5.9 years ago by 141k • written 5.9 years ago by ★ 1.7k
9
votes
7
replies
1.9k
views
Is the sequence quality good enough?
WGS HISEQ4000 QC
5.9 years ago by BioinfGuru ★ 1.7k
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
5.9 years ago by BioinfGuru ★ 1.7k
2
votes
2
replies
2.4k
views
HaplotypeCaller output - All records are non-variant - Have I gone wrong somewhere?
SNP haplotypecaller NON_REF gatk
5.9 years ago by BioinfGuru ★ 1.7k
4
votes
12
replies
2.2k
views
Variant calling on single sample Macaque WGS data - advice please
Variant calling mutect2 haplotypecaller PON
5.9 years ago by BioinfGuru ★ 1.7k
0
votes
3
replies
2.1k
views
MEME result v FIMO result for target annotation
meme fimo annotation
6.3 years ago by BioinfGuru ★ 1.7k
6
votes
10
replies
3.7k
views
Can anyone suggest a RShiny app for displaying RNA-seq results online
rna-seq rshiny
updated 6.4 years ago by ★ 2.9k • written 7.8 years ago by ★ 1.7k
6
votes
8
replies
2.0k
views
Is validation necessary?
pipeline publications validation
updated 11 months ago by 43k • written 6.5 years ago by ★ 1.7k
2
votes
3
replies
2.6k
views
Gene synonyms/aliases - Is there a way to collect them programmatically
gene synonyms alias
6.5 years ago by BioinfGuru ★ 1.7k
0
votes
1
reply
1.7k
views
Transmembrane domain protein structure
protein structure prediction transmembrane
updated 6.5 years ago by ★ 1.9k • written 6.5 years ago by ★ 1.7k
0
votes
0
replies
968
views
Comparing expression of undifferentiated cells using ENCODE - which data sets?
ENCODE RNA-seq
6.9 years ago by BioinfGuru ★ 1.7k
7
votes
7
replies
5.5k
views
Heatmap - with diagonally split tiles
heatmap split
6.9 years ago by BioinfGuru ★ 1.7k
1
vote
1
reply
3.7k
views
MACS2 - centering peaks
MACS2 ChIP-Seq peaks centering
6.9 years ago by BioinfGuru ★ 1.7k
1
vote
3
replies
3.4k
views
Meme: What is the optimal sequence length?
meme sequence length fasta
updated 6.9 years ago by • 0 • written 7.5 years ago by ★ 1.7k
1
vote
2
replies
1.5k
views
simoultaneous chromatin + transcriptional profiling
chromatin transcription assay
updated 6.9 years ago by ★ 2.0k • written 6.9 years ago by ★ 1.7k
54
votes
17
replies
5.8k
views
8 follow
Is annotation of enhancers to nearest gene pointless?
enhancer annotation
updated 11 months ago by 43k • written 6.9 years ago by ★ 1.7k
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 7.0 years ago by 20 • written 7.1 years ago by ★ 1.7k
0
votes
0
replies
1.9k
views
Can I run nucleoatac with a consensus peak file?
nucleoatac ATAC ATAC-seq
7.1 years ago by BioinfGuru ★ 1.7k
1
vote
2
replies
2.7k
views
Nucleoatac - extending broadPeak regions
Nucleoatac ATAC-seq
updated 7.1 years ago by 13k • written 7.1 years ago by ★ 1.7k
0
votes
0
replies
984
views
Where can I find CHIP-seq data for the suprachiasmatic nucleus?
ChIP-Seq suprachiasmatic nucleus
7.4 years ago by BioinfGuru ★ 1.7k
5
votes
7
replies
5.7k
views
Quantile normalisation: raw rpkm or log2rpkm?
rnaseq quantile normalisation
updated 7.6 years ago by 54k • written 7.6 years ago by ★ 1.7k
0
votes
1
reply
3.3k
views
Should I get the mean of 2 log2 transformed RPKM values?
rnaseq log2 rpkm
7.6 years ago by BioinfGuru ★ 1.7k
2
votes
3
replies
2.1k
views
How do I identify tissue specific genes for 1 small part of the brain?
tissue specific genes brain
7.6 years ago by BioinfGuru ★ 1.7k
2
votes
5
replies
7.9k
views
RNA-seq RPKM significance cut off
RNA-seq RPKM cutoff
updated 7.7 years ago by ★ 2.2k • written 7.7 years ago by ★ 1.7k
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 7.8 years ago by 27k • written 7.8 years ago by ★ 1.7k
2
votes
4
replies
2.2k
views
CummeRbund: I can't create a dispersion plot - help please?
RNA-Seq cummeRbund dispersionPlot cuffData class
7.8 years ago by BioinfGuru ★ 1.7k
9
votes
6
replies
3.5k
views
What is the purpose of running Cufflinks without a reference annotation?
cufflinks reference annotation
7.8 years ago by BioinfGuru ★ 1.7k
1
vote
4
replies
2.6k
views
Cuffdiff not performing tss, cds, splicing, promoter or CDS tests
RNA-Seq cuffdiff
7.8 years ago by BioinfGuru ★ 1.7k
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
7.8 years ago by BioinfGuru ★ 1.7k
0
votes
4
replies
2.9k
views
Cuffmerge: error duplicate GFF ID
cuffmerge duplicate error GFF ID
7.8 years ago by BioinfGuru ★ 1.7k
3
votes
4
replies
2.9k
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
7.8 years ago by BioinfGuru ★ 1.7k
38 results • Page 1 of 1
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6