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reads
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2
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Boxplot function not showing all reads length on x-axis
boxplot
reads
fastq
sequencing
rsubread
updated 4.9 years ago by
Wei Shi
★ 3.6k • written 4.9 years ago by
Raito92
▴ 60
2
votes
5
replies
921
views
Software package for RNA-seq reads simulation?
rna-seq
reads
updated 4.9 years ago by
Gordon Smyth
50k • written 4.9 years ago by
Ramiro Magno
▴ 100
0
votes
1
reply
1.2k
views
DEXseq reads all in ambiguous_readpair_position and empty categories
dexseq
reads
6.8 years ago
514028929
• 0
0
votes
2
replies
941
views
DiffBind absence of reads
diffbind
reads
bamfiles
updated 7.0 years ago by
Rory Stark
★ 5.1k • written 7.0 years ago by
kbrnrc
• 0
0
votes
7
replies
1.8k
views
Speeding up or replacing Loops to process Bam Reads
genomicranges
reads
genomicfeatures
Bam
9.1 years ago
gen
▴ 30
2
votes
2
replies
3.1k
views
DESeq: filter out low count reads
deseq
filter
reads
9.3 years ago
ccheung
• 0
0
votes
1
reply
2.1k
views
Rename read-chromosome-names to refseq-chromosome-names.
reads
updated 9.5 years ago by
James W. MacDonald
65k • written 9.5 years ago by
marcovth
• 0
7 results • Page
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Answer: OrgDb for maize
by
James W. MacDonald
65k
``` > library(AnnotationHub) > hub <- AnnotationHub() |===========================| 100% snapshotDate(): 2023-10-23 > query(hu…
Comment: Which input file is used for DGEList in EgdeR?
by
i.atanasoai
• 0
Understood, Thank you very much for the reply, very kind.
Comment: Which input file is used for DGEList in EgdeR?
by
Michael Love
41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Michael Love
41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts
by
Michael Love
41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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