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5
votes
2
replies
8.5k
views
featureCounts, strand specificity, reversely stranded
RNA-Seq
updated 3.1 years ago by 45k • written 9.7 years ago by ▴ 600
0
votes
1
reply
2.2k
views
Comment: C: methylation data, ratios of methylated vs unmethylated reads
9.8 years ago by tonja.r ▴ 600
17
votes
5
replies
18k
views
dispersion of a gene, what does it mean?
RNA-Seq
updated 3.7 years ago by • 0 • written 9.8 years ago by ▴ 600
0
votes
0
replies
18k
views
Comment: C: dispersion of a gene, what does it mean?
9.8 years ago by tonja.r ▴ 600
1
vote
3
replies
2.2k
views
methylation data, ratios of methylated vs unmethylated reads
sequence
updated 3.1 years ago by 45k • written 9.8 years ago by ▴ 600
0
votes
1
reply
2.7k
views
DESEeq differential analysis after PEER normalization
peer ruvseq deseq
updated 3.1 years ago by 45k • written 9.8 years ago by ▴ 600
1
vote
0
replies
6.9k
views
Answer: A: Normalizing For Batch Effect In RNA-Seq Data
9.8 years ago by tonja.r ▴ 600
0
votes
0
replies
3.0k
views
dispersion estimation from DESeq and edgerR
R
updated 3.0 years ago by 45k • written 9.9 years ago by ▴ 600
0
votes
0
replies
2.5k
views
Comment: C: how the data should look like after the normalization
9.9 years ago by tonja.r ▴ 600
1
vote
4
replies
2.5k
views
how the data should look like after the normalization
R
updated 3.0 years ago by 45k • written 9.9 years ago by ▴ 600
1
vote
1
reply
4.0k
views
variance stabilized or log transformed data for DE analysis
RNA-Seq
updated 3.0 years ago by 45k • written 9.9 years ago by ▴ 600
8
votes
7
replies
5.3k
views
PEER normalization after DESeq run
R
updated 3.0 years ago by 45k • written 9.9 years ago by ▴ 600
1
vote
0
replies
2.5k
views
RUVseq interpretation of each method
R
updated 3.0 years ago by 45k • written 9.9 years ago by ▴ 600
1
vote
1
reply
2.9k
views
RUVseq uses the the edgeR differential analysis
R
updated 3.0 years ago by 45k • written 9.9 years ago by ▴ 600
0
votes
0
replies
2.0k
views
edgeR estamateDisp give other results when broken into two sub function
R
updated 3.0 years ago by 45k • written 9.9 years ago by ▴ 600
1
vote
1
reply
2.3k
views
samtools view, overlap with multiple regions
alignment
updated 3.0 years ago by 45k • written 9.9 years ago by ▴ 600
0
votes
1
reply
20k
views
Comment: C: featureCounts strand specificity
9.9 years ago by tonja.r ▴ 600
17
votes
12
replies
20k
views
featureCounts strand specificity
alignment
updated 3.0 years ago by 45k • written 9.9 years ago by ▴ 600
0
votes
2
replies
20k
views
Comment: C: featureCounts strand specificity
9.9 years ago by tonja.r ▴ 600
0
votes
1
reply
20k
views
Comment: C: featureCounts strand specificity
9.9 years ago by tonja.r ▴ 600
1
vote
1
reply
3.7k
views
featurecounts vs samtools view
software-error
updated 3.0 years ago by 45k • written 9.9 years ago by ▴ 600
0
votes
1
reply
3.2k
views
Comment: C: featureCounts of subread
9.9 years ago by tonja.r ▴ 600
1
vote
2
replies
3.2k
views
samtools view with specified regions, different output with and without -F 4
alignment
updated 3.0 years ago by 45k • written 9.9 years ago by ▴ 600
1
vote
5
replies
3.2k
views
featureCounts of subread
R
updated 3.0 years ago by 45k • written 9.9 years ago by ▴ 600
5
votes
1
reply
3.4k
views
DESeq estimateSize factor, if one sample has 0
rna-seq
updated 3.0 years ago by 45k • written 9.9 years ago by ▴ 600
0
votes
1
reply
2.9k
views
check how normalization of count data worked
sequencing
updated 3.0 years ago by 45k • written 9.9 years ago by ▴ 600
0
votes
0
replies
2.7k
views
Comment: Comment: statistical test on count data for differential expression
updated 3.0 years ago by 45k • written 9.9 years ago by ▴ 600
0
votes
0
replies
2.7k
views
Comment: Comment: statistical test on count data for differential expression
updated 3.0 years ago by 45k • written 9.9 years ago by ▴ 600
1
vote
5
replies
2.7k
views
statistical test on count data for differential expression
gene
updated 3.0 years ago by 45k • written 9.9 years ago by ▴ 600
0
votes
1
reply
5.5k
views
Comment: C: H3K4me3 and H3K27ac double peaks near TSS
9.9 years ago by tonja.r ▴ 600
0
votes
0
replies
4.8k
views
Comment: Comment: Average Width Of H3K4Me3 Peaks
updated 3.0 years ago by 45k • written 9.9 years ago by ▴ 600
0
votes
0
replies
1.8k
views
cufflinks several tracks for one gene
cuffdiff Assembly cufflinks
updated 3.0 years ago by 45k • written 9.9 years ago by ▴ 600
0
votes
0
replies
3.7k
views
Comment: C: cufflinks with reference annotation, FPKM for a gene
9.9 years ago by tonja.r ▴ 600
1
vote
2
replies
3.7k
views
cufflinks with reference annotation, FPKM for a gene
RNA-Seq
updated 3.1 years ago by 45k • written 9.9 years ago by ▴ 600
0
votes
1
reply
3.3k
views
Comment: Comment: cufflinks, RPKM for a gene, taking only exons
updated 3.0 years ago by 45k • written 10.0 years ago by ▴ 600
2
votes
3
replies
3.3k
views
cufflinks, RPKM for a gene, taking only exons
RNA-Seq
updated 3.0 years ago by 45k • written 10.0 years ago by ▴ 600
0
votes
0
replies
4.6k
views
Comment: C: chip-seq data for histone, tag count
10.0 years ago by tonja.r ▴ 600
0
votes
1
reply
4.6k
views
Comment: Comment: chip-seq data for histone, tag count
updated 3.0 years ago by 45k • written 10.0 years ago by ▴ 600
3
votes
4
replies
4.6k
views
chip-seq data for histone, tag count
ChIP-Seq
updated 3.0 years ago by 45k • written 10.0 years ago by ▴ 600
0
votes
1
reply
4.4k
views
Comment: Comment: bedtools coverageBed vs samtools mpileup, speed
updated 3.0 years ago by 45k • written 10.0 years ago by ▴ 600
1
vote
4
replies
4.4k
views
bedtools coverageBed vs samtools mpileup, speed
sequencing
updated 3.0 years ago by 45k • written 10.0 years ago by ▴ 600
0
votes
0
replies
10k
views
Comment: Comment: coverage per base using samtools depth and mpileup
updated 3.0 years ago by 45k • written 10.0 years ago by ▴ 600
5
votes
5
replies
10k
views
coverage per base using samtools depth and mpileup
sequencing
updated 3.0 years ago by 45k • written 10.0 years ago by ▴ 600
1
vote
1
reply
10k
views
Answer: C: coverage per base using samtools depth and mpileup
10.0 years ago by tonja.r ▴ 600
0
votes
1
reply
4.1k
views
rsubread: featureCounts, extending ChIP-seq reads, counting the fragments
ChIP-Seq R
updated 3.0 years ago by 45k • written 10.0 years ago by ▴ 600
1
vote
1
reply
2.3k
views
TxDb.Mmusculus.UCSC.mm9.knownGene showing exons with gene_id but there is no such gene
R
updated 3.0 years ago by 45k • written 10.0 years ago by ▴ 600
2
votes
3
replies
5.9k
views
enhancer annotation for mouse mm9
genome
updated 3.0 years ago by 45k • written 10.0 years ago by ▴ 600
2
votes
1
reply
1.7k
views
What does it mean a H4K20me1 has a diffuse profile?
ChIP-Seq
updated 2.9 years ago by 45k • written 10.0 years ago by ▴ 600
0
votes
0
replies
3.6k
views
Comment: Comment: hypergeometric distribution for proximal gene enrichment
updated 2.9 years ago by 45k • written 10.0 years ago by ▴ 600
0
votes
1
reply
3.6k
views
Comment: Comment: hypergeometric distribution for proximal gene enrichment
updated 2.9 years ago by 45k • written 10.1 years ago by ▴ 600
148 results • Page 2 of 3
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