frenkiboy

Is it possible to run masif on small molecule data?

Installation error with python 3.9[BUG]

5

**Describe the bug** When I try to install pySCENIC using python version 3.9 the installation drops with an error It works in python 3.8. The error seems to be related...

Command line has too many arguments

2

With a large database containing many files the base build step dies due to the command line character limit For example, when trying to build a database of complete AlphaFold...

Error during easy-search

1

## Expected Behavior Aligning human AlphaFold proteome to the Mycobacterium tuberculosis proteome ## Current Behavior Index table: counting k-mers /data/local/vfranke/VFranke_Structures/TMP/16012876887949026468/search_tmp/8683525511783924040/structuresearch.sh: line 17: 49775 Illegal instruction $RUNNER "$MMSEQS" prefilter "${QUERY_PREFILTER}" "${TARGET_PREFILTER}${INDEXEXT}"...

findFeatureComb with one input element produces error when use.names=TRUE library(GenomicRanges) library(genomation) tab.test = system.file('unitTests/tab.test1', package='genomation') #1. test regular bed input r1 = readGeneric(tab.test) l1 = GRangesList(r1 = r1) comb1 =...

Negative coverage values and is.noCovNA=T give wrong results

2

when the target vector is negative (i.e. negative fold changes), is.noCovNA gives wrong results - it converts all < 0 values to NA

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.

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