Bioconductor ATAC

Showing : ATAC • reset

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diffbind atac

6.9 years ago niu.shengyong • 0

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6.1k

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Chipseq DNAseq ATAC bayespeak narrowpeaks

updated 8.9 years ago by Gordon Smyth 50k • written 8.9 years ago by samuel collombet ▴ 140

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1.4k

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limma edger atac atac-seq

updated 4.1 years ago by Aaron Lun ★ 28k • written 4.1 years ago by pgugger ▴ 70

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1.7k

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ATACseqQC ATAC ATACseq software error Tutorial

updated 4.8 years ago by Steve Lianoglou ★ 13k • written 4.8 years ago by mbasam • 0

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ATAC differential binding analysis no replicates DEseq2 chromatin

7.1 years ago BioinfGuru ▴ 20

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2.8k

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atac-seq atac deseq2 sva combat

updated 7.1 years ago by Michael Love 41k • written 7.2 years ago by g.atla ▴ 10

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928

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Diffbind ATAC batch correction blocking factor

updated 4.7 years ago by Rory Stark ★ 5.1k • written 4.7 years ago by rm1238 • 0

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1.2k

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diffbind atac

updated 3.9 years ago by Rory Stark ★ 5.1k • written 3.9 years ago by lindsaynhayes • 0

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2.2k

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diffbind atac

updated 5.2 years ago by Rory Stark ★ 5.1k • written 5.2 years ago by paz2005 • 0

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759

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deseq2 design formula design matrix edgeR ATAC

updated 4.3 years ago by Gordon Smyth 50k • written 4.4 years ago by corinne_hutfilz • 0

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661

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rna-seq Read10X_h5 atac modalities

updated 12 months ago by James W. MacDonald 65k • written 12 months ago by Cynthia • 0

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subread featurecounts atac

updated 5.0 years ago by Wei Shi ★ 3.6k • written 5.0 years ago by aurel.nagy ▴ 10

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545

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r DiffBind ATAC

updated 4.1 years ago by Rory Stark ★ 5.1k • written 4.1 years ago by lindsaynhayes • 0

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1.3k

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diffbind ATACseq ATAC counts differential analysis

updated 5.1 years ago by Rory Stark ★ 5.1k • written 5.1 years ago by pgontarz ▴ 10

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641

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ATAC DiffBind ATACSeq

updated 14 months ago by Rory Stark ★ 5.1k • written 14 months ago by Hadar • 0

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1.4k

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Diffbind Atac adapters

updated 7.1 years ago by Rory Stark ★ 5.1k • written 7.1 years ago by BioinfGuru ▴ 20

16 results • Page 1 of 1

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Comment: Which input file is used for DGEList in EgdeR? by Michael Love 41k

"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…

Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Michael Love 41k

These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…

Comment: DEG with low counts by Michael Love 41k

These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…

Comment: DESeq filtering specific to contrasts by Michael Love 41k

If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…

Comment: Estimating Cell Counts for EPIC V2 array data by normawiedman059 • 0

0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…

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A: Docker container with bioconductor and devtools

Answer: OrgDb for maize

Comment: significant difference of p-values with dream() after updating VariancePartition

How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output

Comment: DEXSeq DEXSeqDataSet count matrix duplication

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