Bioconductor Genome

Showing : Genome • reset

votes

replies

2.6k

views

txdb genome exons

updated 4.7 years ago by Martin Morgan 25k • written 4.7 years ago by Bogdan ▴ 670

votes

1.9k

views

Genome bwamem ChIPSeqData index

updated 14 months ago by ATpoint ★ 4.0k • written 14 months ago by Maka • 0

votes

replies

1.9k

views

annotation gff3 gff genome

updated 4.6 years ago by Michael Lawrence ★ 11k • written 4.6 years ago by mictadlo ▴ 10

votes

replies

1.2k

views

Genome readVcf VariantAnnotation

3.1 years ago naive • 0

votes

replies

1.2k

views

r build genome chicken-sheme

8.5 years ago pertille • 0

votes

replies

1.1k

views

multiplealignment genome

5.6 years ago Giuseppe ▴ 20

votes

replies

1.1k

views

Genome GWASdata

3.2 years ago Jocelyn • 0

vote

1.0k

views

Gviz R UCSC Tracks genome locusplot

updated 4.5 years ago by Robert Ivanek ▴ 730 • written 4.5 years ago by s.koturan • 0

votes

replies

984

views

Alignment Genome

2.5 years ago Charles Plessy ▴ 180

votes

replies

981

views

annotation genome hg38 TxDb.Hsapiens.UCSC.hg38.knownGene BSgenome.Hsapiens.UCSC.hg38

updated 4.2 years ago by kayla.interdonato ▴ 160 • written 4.2 years ago by jam526 • 0

votes

replies

910

views

single cell bioinformatics genome sequencing Job

4.6 years ago jmaanaki • 0

vote

replies

872

views

genome novel package release

updated 5.2 years ago by James W. MacDonald 65k • written 5.2 years ago by pertille • 0

votes

replies

841

views

single cell genome cancer Job

4.9 years ago jmaanaki • 0

votes

replies

645

views

build genome

13 months ago Dmitry • 0

votes

156

views

ensembldb transcriptome genome coordinateconversion

updated 23 days ago by Michael Love 41k • written 26 days ago by saadmurtazakhan ▴ 10

15 results • Page 1 of 1

Recent ...

Replies

Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0

Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…

Comment: PCA plot suggestions by JKim • 0

cross post: https://www.biostars.org/p/9593486/

Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k

You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k

You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…

Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0

My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…

Votes

Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2

Answer: Use of negative binomial model for exponential decay rate estimation using DESeq

C: null model and DEXSeqDataSet object in DEXSEQ

A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?

A: How to explain how DESeq2 works to someone with zero bioinformatics background?

Awards • All

Scholar to James W. MacDonald 65k

Supporter to JKim • 0