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Recent Replies
Comment: How to remove unknown batch-batch effects from GEO datasets
by
2317711200
•
0
Thank you very much for your response.
Answer: How to remove unknown batch-batch effects from GEO datasets
by
Gordon Smyth
★
5.6k
removeBatchEffect() wouldn't produce the outlier effect that you show on the right unless there was something seriously wrong with the batc…
Answer: How to get subset of a Seurat object based on metadata?
by
fracarb8
▴
940
To keep the subset call as clean as possible, you can:
Idents(skin) <- "predicted_cell_type"
cell_values <- c("0:CD8 T cell")
…
Answer: How to remove unknown batch-batch effects from GEO datasets
by
2317711200
•
0
R codes：
library(tidyverse)
####数据获取####
#引文
#citation(package = "GEOquery")
#数据提取
GSE53625_matrix<-GEOquery::getGEO(GEO = "GSE5362…
Answer: Any tips in landing a bioinformatic job?
by
iraun
5.9k
Hi Jorge!
In addition to what has already been said, I found my first bioinformatics job in Spain (Barcelona), using this webpage: [http…
Comment: How to remove unknown batch-batch effects from GEO datasets
by
2317711200
•
0
It is a great honor to receive your response.
The data in question is sourced from GSE53625. While using arrayQualityMetrics to assess the…
Answer: Extract data from Signac RegionMatrix?
by
Chironex
▴
40
object@assays$ATAC@positionEnrichment$my_region_matrix
and also
object@assays$ATAC@positionEnrichment$my_region_matrix$condit…
Comment: Any tips in landing a bioinformatic job?
by
ATpoint
70k
Great answer, narrowing it down the the key points!
Comment: How to remove unknown batch-batch effects from GEO datasets
by
ATpoint
70k
The righthand plot might be totally fine once you remove that one outlier on the left, try that first. The batch effect manifesting along P…
Comment: using CITE-seq data to cluster single cells
by
ATpoint
70k
If it is really just two genes then why not just plotting logcounts of gene1 vs logcounts of gene2 as in a FACS scatter plot and see whethe…
Comment: How to remove unknown batch-batch effects from GEO datasets
by
2317711200
•
0
As a beginner, I hope to receive professional answers. If necessary, I can provide rewards and R code.
Answer: Align miRNA library (small RNA-seq) without trimming
by
ATpoint
70k
For miRNA you should trim the data to the actual expected miRNA length (20-something bp, I would need to look up the exact value). Reason i…
Comment: boxplot issue
by
ATpoint
70k
Please get used to make your question reproducible and precise, meaning provide example data and reduce code to a minimum.
Answer: Total No of Genes of GENCODE Release 43
by
ATpoint
70k
As I said, I assume that you are doing something on old/overwritten variables or a wrong GTF. This is how it is:
a<-rtracklayer::i…
Answer: Any tips in landing a bioinformatic job?
by
Vincent Laufer
★
2.6k
Do you have a public facing github page (or equivalent) that provides examples of bioinformatics workflows you've created?
For myself, if …
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