misha-package: Toolkit for analysis of genomic data

In misha: Toolkit for Analysis of Genomic Data

Toolkit for analysis of genomic data

Description

'misha' package is intended to help users to efficiently analyze genomic data achieved from various experiments.

Details

For a complete list of help resources, use library(help = "misha").

The following options are available for the package. Use 'options' function to alter the value of the options.

NAME	DEFAULT	DESCRIPTION
gmax.data.size	AUTO	Auto-configured based on system RAM and processes.
		Formula: min((RAM * 0.7) / gmax.processes, 10GB).
		Controls max in-memory result buffer size for streaming/sampling.
		Operations like gextract, gscreen use this as upper bound.
gbig.intervals.size	1000000	Threshold for converting interval sets to disk-based
		"big" format. When interval count exceeds this, intervals
		are stored per-chromosome instead of all in memory.
		Note: Independent of gmax.data.size (different purposes).
gmax.mem.usage	10000000	Maximal memory consumption of all child
		processes in KB before the limiting algorithm is invoked.
gmax.processes	AUTO	Auto-configured to min(32, 70% of CPU cores).
		Maximal number of processes for multitasking.
gmax.processes2core	2	Maximal number of processes per CPU core for multitasking
gseq.extract.probe.usec	100	gseq.extract times its first reads
		and distributes across processes when the measured cost per
		interval reaches this many microseconds. 0 always distributes,
		a large value never does.
gmin.scope4process	10000	Minimal scope range (for 2D: surface) assigned to a process
		in multitasking mode.
gbuf.size	1000	Size of track expression values buffer.
gmultitask.max.records.factor	64	Multiplier to inflate multitask
		max_records estimates to avoid under-allocation.
gtrack.chunk.size	100000	Chunk size in bytes of a 2D track. If '0' chunk size
		is unlimited.
gtrack.num.chunks	0	Maximal number of 2D track chunks simultaneously stored
		in memory.
gmultitasking	TRUE	Enable/disable automatic parallelization. Some functions
		may choose single-threaded mode for very small workloads.
gpermissions.umask	"0007"	umask applied around misha's own writes
		into a database: 660 files, 770 directories - group-writable,
		no world access - matching what the C++ layer enforces. Set to
		"0002" for the world-readable 664/775 that misha produced before
		5.11.21, or to NULL to leave the process umask untouched. The
		umask is restored as soon as the write returns.

More information about the options can be found in 'User manual' of the package.

Author(s)

Maintainer: Aviezer Lifshitz [e-mail]

Authors:

• Aviezer Lifshitz [e-mail]

• Misha Hoichman [e-mail]

• Eitan Yaffe [e-mail]

• Amos Tanay [e-mail]

Other contributors:

• Weizmann Institute of Science [copyright holder]

See Also

Useful links:

• https://tanaylab.github.io/misha/

• https://github.com/tanaylab/misha

• Report bugs at https://github.com/tanaylab/misha/issues

misha documentation built on Aug. 24, 2026, 5:14 p.m.