genomation

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intersectScoreMatrixList gives wrong result, if nbins=1 in ScoreMatrixList

3

When intersectScoreMatrixList is used after a ScoreMatrixList with nbins=1, somewhere along the code, the rownames are dropped from the matrix, and the intersectScoreMatrixList gives empty ScoreMatrix objects.

frenkiboy

Adding filtering capabilities for bam data (e.g. take only reads from the - strand)

1

frenkiboy

Allow antisymmetric data [Feature request]

1

Hi Altuna, In some cases the signal supplied to ScoreMatrix as "target" is antisymmetric under strand reversal. In our case it is a difference between signal mapped to the +...

balwierz

frenkiboy

add seqlengths argument to ScoreMatrixList and ScoreMatrix

2

When the targets are GRaneges, the resulting Rle can have different lengths, resulting in some windows being dropped in a certain set

frenkiboy

PAR-CLIP or BS-seq relies on nucleotide mismatch frequencies as genome-wide scores. We can use pileup function from samtools to extract those frequencies to a scoreMatrix object???

al2na

frenkiboy

Add the new randomization algorithm which keeps the distribution of feature and interfeature distances

frenkiboy

Annotation of genomic features object

2

Maybe our function should work also with genomic features objects?

frenkiboy

ScoreMatrixBin not working in version 1.35.0

1

I am trying to run your devel version (1.35.0) of genomation , but the ScoreMatrixBin function gives me an error (I have Matrix 1.7-0 installed): > library(genomation) > data(cage) >...

shuye2009