Bioconductor KaryoploteR

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BSgenome.Athaliana.TAIR.TAIR10. karyoploteR BSgenome

updated 18 months ago by James W. MacDonald 65k • written 18 months ago by rtt100 • 0

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karyoploter

updated 4.6 years ago by bernatgel ▴ 150 • written 4.6 years ago by Aditya ▴ 160

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karyoploter

updated 6.6 years ago by bgel ▴ 10 • written 6.6 years ago by spr ▴ 10

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809

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KaryoploteR

updated 3.6 years ago by Kevin Blighe ★ 3.9k • written 3.6 years ago by mpigozzi • 0

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858

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KaryoploteR

6.8 years ago Radek ▴ 90

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427

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GenomicFeatures karyoploteR TxDb.Hsapiens.UCSC.hg19.knownGene

12 months ago Shreyash • 0

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software error R bsgenome karyoploter

updated 6.5 years ago by bernatgel ▴ 150 • written 6.5 years ago by kirannbishwa01 ▴ 10

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838

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karyoploteR

updated 5.0 years ago by bernatgel ▴ 150 • written 5.0 years ago by saeed Ur Rehman • 0

8 results • Page 1 of 1

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Answer: FGSEA pre-ranked input in increasing order or decreasing by alserg ▴ 240

The genes are automatically ordered within `fgsea`, there is no need to sort them manually.

Comment: Differential peaks that were not identified in diffbind were identified in diseq by ATpoint ★ 4.0k

Make an MAplot. There is almost certainly an issue with normalization here given the very biased distribution of logFCs as in this Volcano.

Comment: significant difference of p-values with dream() after updating VariancePartition by gabriel.hoffman ▴ 100

See variancePartition updates for [v1.33.11](https://diseaseneurogenomics.github.io/variancePartition/news/index.html#variancepartition-133…

Comment: A ComBat-seq issue: the covariates are confounded by W. Evan Johnson ▴ 850

This is only partially confounded because there is overlap between the batches -- they both have GFP controls that can be used to remove ba…

Answer: Different number of exons in reference genome affects DEXSeq analysis by Alejandro Reyes ★ 1.9k

Likely the new annotation that you are using has more annotated isoforms, and thus the exons are splitted into more disjoint exonic bins. I…

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Comment: DEXSeq DEXSeqDataSet count matrix duplication

Comment: Error in champ.load(): The following specified files do not exist

Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos

Using GRanges and IRanges to simply get all chromosome data

A: Using GRanges and IRanges to simply get all chromosome data

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