Showing : filtering • reset
3
votes
5
replies
529
views
How to analyze pre-processed RNA-Seq data from GEO based on the deseq R package for filtering and DE analysis
deseq rna-seq filtering DE deseq2
updated 2.1 years ago by 36k • written 2.1 years ago by ▴ 780
0
votes
0
replies
281
views
Filter TCGAbiolinks by Gene in Query
tcgabiolinks filtering gdc TCGABiolinks rnaseq
2.3 years ago jam526 • 0
2
votes
4
replies
697
views
Filtering, minimum sample number, and condition in edgeR
edger filtering
updated 3.5 years ago by 7.8k • written 3.5 years ago by ▴ 20
0
votes
1
reply
289
views
How to keep the genes whose counts are equal or greater than 10
deseq2 filtering
updated 3.5 years ago by 59k • written 3.5 years ago by • 0
1
vote
1
reply
348
views
DeSeq2 independant filtering barely removes any genes
deseq2 differential gene expression filtering
updated 3.9 years ago by 36k • written 3.9 years ago by • 0
1
vote
2
replies
495
views
Filtering Rna-seq counts
rna-seq filtering
updated 4.0 years ago by 45k • written 4.0 years ago by ▴ 20
4
votes
12
replies
3.8k
views
Filtering step for differential analysis in edgeR
r edger differential gene expression filtering bioconductor
updated 4.0 years ago by 45k • written 4.0 years ago by ▴ 90
4
votes
8
replies
846
views
edgeR error when trying to filter peaks with low read counts
edger R filtering
4.1 years ago camerond • 0
0
votes
2
replies
587
views
Filtering genes with a minimum number of counts between samples
DESeq2 filtering
updated 4.3 years ago by 36k • written 4.3 years ago by ▴ 40
1
vote
1
reply
716
views
Filtering a BED file according to genomic annotation
bed files bedtools filtering chipseq
updated 4.4 years ago by ★ 27k • written 4.4 years ago by ▴ 60
0
votes
2
replies
1.1k
views
DiffBind remove low count intervals for differential analysis
diffbind filtering
4.4 years ago gasta88 • 0
0
votes
2
replies
573
views
DiffBind dba.report inconsistent output when using filter parameters
diffbind dba.report filtering
4.5 years ago konstantopoulos • 0
1
vote
3
replies
3.1k
views
DESeq2: How to manually perform filtering and outlier detection?
deseq2 filtering outliers count outliers
updated 4.8 years ago by 13k • written 4.8 years ago by ▴ 10
1
vote
6
replies
1.1k
views
Nonspecific filtering of microarray data
microarray affymetrix microarrays pre-filtering filtering nonspecific filtering
updated 5.0 years ago by 13k • written 5.0 years ago by • 0
2
votes
2
replies
626
views
Limma filtering based on treatment group
limma filtering
updated 5.0 years ago by 13k • written 5.0 years ago by ▴ 50
3
votes
4
replies
738
views
Any way to detach or simplify nested GRangesList ?
grangeslist filtering r
5.6 years ago Jurat Shahidin ▴ 70
1
vote
2
replies
1.5k
views
edgeR filtering: how to remove meta tags and lowly expressed reads (cpm)
edger filtering cpm
updated 5.7 years ago by 45k • written 5.7 years ago by • 0
4
votes
4
replies
1.0k
views
Filtering after a contrast
deseq2 r filtering bioconductor
updated 5.8 years ago by 13k • written 5.8 years ago by • 0
0
votes
1
reply
718
views
Does the normalization pipeline for scran include filtering out genes with low counts?
filtering scran
updated 5.8 years ago by ★ 27k • written 5.8 years ago by • 0
8
votes
11
replies
6.1k
views
Filtering of RNA-seq data in EdgeR
rnaseq edger filtering
updated 5.9 years ago by ▴ 10 • written 6.0 years ago by ▴ 10
5
votes
12
replies
1.2k
views
Filtering before the linear modelling and empirical bayes steps
DEG Limma Filtering
updated 6.1 years ago by 7.8k • written 6.2 years ago by ▴ 20
2
votes
4
replies
1.6k
views
Analysis of Affymetrix Mouse Gene 2.0 ST arrays
affymetrix limma filtering
updated 7.0 years ago by 59k • written 7.0 years ago by • 0
2
votes
7
replies
2.0k
views
Different filters with edgeR
edger filtering
7.1 years ago cpcantalapiedra • 0
3
votes
10
replies
1.7k
views
Question about converting rownames of an expression dataset to their corresponding gene symbols
filtering bioconductor genesymbols expressionset
7.2 years ago svlachavas ▴ 780
24 results • Page 1 of 1
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Answer: Using featureCounts and downloading Rsubread by James W. MacDonald 59k
You need to tell `BiocManager;;install` that you want to install the `Rsubread` package. ``` BiocManager::install("Rsubread") library(…
Comment: featureCounts: 0% successfully assigned fragments by KMS • 0
Dear ATpoint I am exactly looking for read/gene count from BAM/SAM file either through ht-seq or feature count feature count giving me 0% s…
Answer: Get MANE transcripts from TxDb.Hsapiens.UCSC.hg38.knownGene by James W. MacDonald 59k
There is the ncbiRefSeqSelect table that has the MANE and RefSeq Select transcripts. It's not just the MANE though. ``` > z <- makeTxDb…
Comment: Handling of missing values in limma by AyHi • 0
Thank you, Gordon, for your reply. I used sum(is.na(lmfit)) after lmFit, but somewhat it indicated there was no NA observations even when…
Comment: merging VCF files by lesefo6448 • 0
You can use this VCF Merger Software if you want to Merge VCF files into one file. this Software easily Merge your multiple VCF files with…
Votes
Answer: Load packages when using BatchtoolsParam
Comment: Load packages when using BatchtoolsParam
Answer: edgeR: the F-statistics changed after removing lowly expressed gene
Answer: edgeR: the F-statistics changed after removing lowly expressed gene
A: DESeq2: thousands of NA for pvalues?
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