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Gencode
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reset
4
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3
replies
1.6k
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Selecting Correct Set of Gene IDs from Mouse Gencode GFF3 for RNA Seq Analysis (Removing Genes without symbols)
deseq2
tximport
org.mm.eg.db
gencode
6.1 years ago
pvd2107
▴ 30
4
votes
7
replies
5.9k
views
convert featureCounts's gene ID to entrez gene id
biomart
rsubread
gencode
updated 5.5 years ago by
James W. MacDonald
65k • written 5.5 years ago by
YinCY
▴ 20
3
votes
3
replies
1.3k
views
Recount data for unannotated genes
recount
RNAseq
gencode
lncRNA
gene annotation
updated 5.0 years ago by
chris.wilks
▴ 70 • written 5.1 years ago by
francesco.gandolfi
▴ 20
3
votes
5
replies
1.8k
views
Include and implement a new reference genome option in the R package BSgenome for downstream variant calling analysis
bsgenome
variant calling
whole exome sequence
gencode
reference genome
updated 5.7 years ago by
Hervé Pagès
16k • written 5.7 years ago by
svlachavas
▴ 830
2
votes
0
replies
3.3k
views
News:
Gencode GFF3 and FASTA files now available via AnnotationHub
AnnotationHub
Gencode
GFF3
FASTA
News
8.7 years ago
Sonali Arora
▴ 390
5 results • Page
1 of 1
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Replies
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
by
Michael Love
41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Comment: Trying to use enrichGO
by
fernanda.backsouza
▴ 10
With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
swbarnes2
★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error
by
James W. MacDonald
65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Votes
Answer: Adding a group of samples reduces DEGs in other groups
Answer: Gene set analysis: GSVA, Z-Score, and fold-changes
Answer: FilterByExpr low counts with small sample size
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
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