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questions
0
votes
1
reply
4.4k
views
limma goana or kegg
R
goana
updated 21 months ago by
Ram
43k • written 8.3 years ago by
tonja.r
▴ 600
0
votes
1
reply
2.2k
views
UCSC mouse gene annotation mm9 shows speculative genes
R
updated 19 months ago by
Ram
43k • written 8.6 years ago by
tonja.r
▴ 600
1
vote
1
reply
2.8k
views
samtools mpileup for multiple regions output in different files
sequencing
updated 19 months ago by
Ram
43k • written 8.6 years ago by
tonja.r
▴ 600
3
votes
4
replies
3.2k
views
installing blat for homer on os x
software-error
blast
updated 22 months ago by
Ram
43k • written 9.1 years ago by
tonja.r
▴ 600
2
votes
6
replies
6.8k
views
SE reads in fr-firststrand, fr-secondstrand
rna-seq
sequencing
updated 6 months ago by
xiaoleiusc
▴ 140 • written 8.2 years ago by
tonja.r
▴ 600
2
votes
1
reply
2.8k
views
bioconductor promoter annotation for mm9
R
genome
updated 19 months ago by
Ram
43k • written 8.6 years ago by
tonja.r
▴ 600
1
vote
1
reply
5.2k
views
would it be a good idea to normalize log2 fold changes with loess?
RNA-Seq
ChIP-Seq
updated 21 months ago by
Ram
43k • written 8.3 years ago by
tonja.r
▴ 600
3
votes
2
replies
6.0k
views
DESeq PCA plot and edgeR MDS plot
R
updated 20 months ago by
Ram
43k • written 8.5 years ago by
tonja.r
▴ 600
6
votes
7
replies
5.2k
views
RSeQC infer_experiment.py results interpretation for cuffdiff and featureCounts
RNA-Seq
updated 21 months ago by
Ram
43k • written 8.3 years ago by
tonja.r
▴ 600
4
votes
11
replies
7.3k
views
demultiplexing with fastq having barcode and primer sequence
sequencing
next-gen
demultiplex
7.5 years ago by
tonja.r
▴ 600
4
votes
2
replies
3.1k
views
demultiplexing with fastq but without barcode read fastq
next-gen
sequencing
updated 7.5 years ago by
charbo24
▴ 40 • written 7.5 years ago by
tonja.r
▴ 600
1
vote
3
replies
3.8k
views
single end reads, reverse and forward primer
next-gen
updated 7.5 years ago by
dariober
14k • written 7.5 years ago by
tonja.r
▴ 600
2
votes
6
replies
4.8k
views
H3K4me3 and H3K27ac double peaks near TSS
ChIP-Seq
updated 19 months ago by
Ram
43k • written 8.6 years ago by
tonja.r
▴ 600
0
votes
3
replies
2.5k
views
chip-seq (histone modifications) and rna-seq data for benchmarking
RNA-Seq
ChIP-Seq
updated 21 months ago by
Ram
43k • written 8.3 years ago by
tonja.r
▴ 600
0
votes
0
replies
1.8k
views
dispersion and variability of samples/replicates in DESeq2
RNA-Seq
updated 2.0 years ago by
Ram
43k • written 8.2 years ago by
tonja.r
▴ 600
1
vote
3
replies
2.4k
views
p-value distribution of edger or deseq2
RNA-Seq
updated 21 months ago by
Ram
43k • written 8.2 years ago by
tonja.r
▴ 600
0
votes
3
replies
2.8k
views
encode data for RNAseq, type of library
RNA-Seq
updated 21 months ago by
Ram
43k • written 8.3 years ago by
tonja.r
▴ 600
2
votes
2
replies
2.6k
views
high fold changes due to the low counts
RNA-Seq
updated 20 months ago by
Ram
43k • written 8.5 years ago by
tonja.r
▴ 600
0
votes
1
reply
2.4k
views
GFOLD diff input
RNA-Seq
updated 20 months ago by
Ram
43k • written 8.5 years ago by
tonja.r
▴ 600
0
votes
1
reply
1.8k
views
GFOLD posterior distribution
RNA-Seq
R
updated 20 months ago by
Ram
43k • written 8.5 years ago by
tonja.r
▴ 600
0
votes
9
replies
3.9k
views
meta analysis of p values from deseq2 output
RNA-Seq
updated 21 months ago by
Ram
43k • written 8.3 years ago by
tonja.r
▴ 600
2
votes
2
replies
2.0k
views
looking for chip-seq histone marks and rna-seq data
RNA-Seq
ChIP-Seq
updated 2.6 years ago by
Ram
43k • written 8.3 years ago by
tonja.r
▴ 600
5
votes
2
replies
7.7k
views
featureCounts, strand specificity, reversely stranded
RNA-Seq
updated 21 months ago by
Ram
43k • written 8.3 years ago by
tonja.r
▴ 600
17
votes
5
replies
17k
views
dispersion of a gene, what does it mean?
RNA-Seq
updated 2.4 years ago by
ED
• 0 • written 8.4 years ago by
tonja.r
▴ 600
1
vote
3
replies
1.8k
views
methylation data, ratios of methylated vs unmethylated reads
sequence
updated 20 months ago by
Ram
43k • written 8.4 years ago by
tonja.r
▴ 600
0
votes
1
reply
2.4k
views
DESEeq differential analysis after PEER normalization
peer
ruvseq
deseq
updated 20 months ago by
Ram
43k • written 8.4 years ago by
tonja.r
▴ 600
0
votes
0
replies
2.7k
views
dispersion estimation from DESeq and edgerR
R
updated 20 months ago by
Ram
43k • written 8.6 years ago by
tonja.r
▴ 600
1
vote
4
replies
2.0k
views
how the data should look like after the normalization
R
updated 20 months ago by
Ram
43k • written 8.5 years ago by
tonja.r
▴ 600
1
vote
1
reply
3.6k
views
variance stabilized or log transformed data for DE analysis
RNA-Seq
updated 20 months ago by
Ram
43k • written 8.5 years ago by
tonja.r
▴ 600
8
votes
7
replies
4.4k
views
PEER normalization after DESeq run
R
updated 20 months ago by
Ram
43k • written 8.5 years ago by
tonja.r
▴ 600
1
vote
0
replies
2.3k
views
RUVseq interpretation of each method
R
updated 20 months ago by
Ram
43k • written 8.5 years ago by
tonja.r
▴ 600
1
vote
1
reply
2.6k
views
RUVseq uses the the edgeR differential analysis
R
updated 20 months ago by
Ram
43k • written 8.5 years ago by
tonja.r
▴ 600
0
votes
0
replies
1.8k
views
edgeR estamateDisp give other results when broken into two sub function
R
updated 20 months ago by
Ram
43k • written 8.5 years ago by
tonja.r
▴ 600
1
vote
1
reply
2.1k
views
samtools view, overlap with multiple regions
alignment
updated 20 months ago by
Ram
43k • written 8.5 years ago by
tonja.r
▴ 600
14
votes
12
replies
17k
views
featureCounts strand specificity
alignment
updated 20 months ago by
Ram
43k • written 8.5 years ago by
tonja.r
▴ 600
1
vote
1
reply
3.2k
views
featurecounts vs samtools view
software-error
updated 20 months ago by
Ram
43k • written 8.5 years ago by
tonja.r
▴ 600
1
vote
2
replies
2.7k
views
samtools view with specified regions, different output with and without -F 4
alignment
updated 20 months ago by
Ram
43k • written 8.5 years ago by
tonja.r
▴ 600
1
vote
5
replies
2.8k
views
featureCounts of subread
R
updated 20 months ago by
Ram
43k • written 8.5 years ago by
tonja.r
▴ 600
5
votes
1
reply
3.1k
views
DESeq estimateSize factor, if one sample has 0
rna-seq
updated 20 months ago by
Ram
43k • written 8.6 years ago by
tonja.r
▴ 600
0
votes
1
reply
2.6k
views
check how normalization of count data worked
sequencing
updated 19 months ago by
Ram
43k • written 8.6 years ago by
tonja.r
▴ 600
1
vote
5
replies
2.3k
views
statistical test on count data for differential expression
gene
updated 19 months ago by
Ram
43k • written 8.6 years ago by
tonja.r
▴ 600
0
votes
0
replies
1.6k
views
cufflinks several tracks for one gene
cuffdiff
Assembly
cufflinks
updated 19 months ago by
Ram
43k • written 8.6 years ago by
tonja.r
▴ 600
1
vote
2
replies
3.4k
views
cufflinks with reference annotation, FPKM for a gene
RNA-Seq
updated 20 months ago by
Ram
43k • written 8.6 years ago by
tonja.r
▴ 600
2
votes
3
replies
2.9k
views
cufflinks, RPKM for a gene, taking only exons
RNA-Seq
updated 19 months ago by
Ram
43k • written 8.6 years ago by
tonja.r
▴ 600
3
votes
4
replies
4.2k
views
chip-seq data for histone, tag count
ChIP-Seq
updated 19 months ago by
Ram
43k • written 8.6 years ago by
tonja.r
▴ 600
1
vote
4
replies
3.7k
views
bedtools coverageBed vs samtools mpileup, speed
sequencing
updated 19 months ago by
Ram
43k • written 8.6 years ago by
tonja.r
▴ 600
5
votes
5
replies
9.3k
views
coverage per base using samtools depth and mpileup
sequencing
updated 19 months ago by
Ram
43k • written 8.6 years ago by
tonja.r
▴ 600
0
votes
1
reply
3.6k
views
rsubread: featureCounts, extending ChIP-seq reads, counting the fragments
ChIP-Seq
R
updated 19 months ago by
Ram
43k • written 8.6 years ago by
tonja.r
▴ 600
1
vote
1
reply
2.1k
views
TxDb.Mmusculus.UCSC.mm9.knownGene showing exons with gene_id but there is no such gene
R
updated 19 months ago by
Ram
43k • written 8.6 years ago by
tonja.r
▴ 600
2
votes
3
replies
5.3k
views
enhancer annotation for mouse mm9
genome
updated 19 months ago by
Ram
43k • written 8.6 years ago by
tonja.r
▴ 600
85 results • Page
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