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ATACseq
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reset
2
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5
replies
830
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Trying to convert ATACseq annotations of non-model species into human orthologs, but not sure of what to do.
genomes
ATACSeq
6 months ago • updated 5 months ago
ronin
• 0
0
votes
4
replies
665
views
Differential peaks that were not identified in diffbind were identified in diseq2
DiffBind
DESeq2
ATACSeq
11 months ago
lonn
• 0
0
votes
0
replies
620
views
FindOverlaps, makeVennDiagram and "others"
ATACSeq
peaks
ATAC
ChIPpeakAnno
9 months ago
Raghad
• 0
0
votes
0
replies
424
views
DIFFBIND : beginner questions, sex, multiple phenotypes, etc...
DiffBind
ATACSeq
11 months ago
Pierre Lindenbaum
▴ 10
0
votes
0
replies
217
views
diffbind covariates
DiffBind
ATACSeq
updated 4 months ago by
Michael Love
43k • written 4 months ago by
Alpesh Querer
▴ 220
0
votes
1
reply
574
views
Spike-in normalization method in ATACseq
sperm
Drosophila_melanogaster
ATACSeq
Normalization
SpikeIn
updated 4 months ago by
ATpoint
★ 4.7k • written 4 months ago by
Katerina
• 0
6 results • Page
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Answer: affy::rma results doesn't match with ncbi website
by
ATpoint
★ 4.7k
Exact OMCIS reproduction down to the values without code and software version is borderline impossible. Either use the values as provided o…
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
by
James W. MacDonald
68k
You've got it backwards. It should be ``` adult_res_df$symbol <- mapIds(org.Rn.eg.db, keys = rownames(adult_res_df), column = "ENSEMBL"…
Comment: DESeq2 swap ensembl gene id rownames with gene symbol column
by
Erika
• 0
Alternatively, you could have added a column with the common gene names. Assuming your dataframe `df` was created using `DESeq()`, somethin…
Answer: Clarification on GOALL / GO2ALLORFs mapping
by
James W. MacDonald
68k
It appears that 'negative regulation of glycogen biosynthesis' has an 'is a' relationship with 'glycogen biosynthetic process' https://www.…
Comment: Can't post a question?
by
DavideSant
• 0
Thank you, this was super useful!
Votes
Comment: Can't post a question?
Answer: Limma - Complex 2-way multi-level contrast with paired samples
Answer: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks
Help with creation of an OrgDB package and conduction of a bioinformatical analysis of gene expression
Answer: Loading Ensembl 98 EnsDb from Annotation Hub fails with database disk image malf
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