Paket: sideretro (1.1.6-2)

[ Källkod: sideretro  ]

pipeline for detecting Somatic Insertion of DE novo RETROcopies

sideRETRO is a bioinformatics tool designed for the detection of somatic retrocopy insertions, also known as retroCNVs, in whole genome sequencing (WGS) and whole exome sequencing (WES) data.

Retrocopies, also known as processed pseudogenes, are sequences derived from protein-coding genes, generated by the duplication of these genes through the transposition of their mature messenger RNA via the LINE-1 enzymatic machinery. Retrocopies can be fixed, meaning they are present in all genomes of a given species (including the species' reference genome), or unfixed (polymorphic, germline, or somatic), in which case they are referred to as retroCNVs. While fixed retrocopies have received considerable attention in the scientific community, knowledge of retroCNVs remains limited, largely due to the lack of specialized bioinformatics tools for their identification and annotation in DNA sequencing data.

sideRETRO is a dedicated computational algorithm that detects retrocopies absent from the reference genome but present in WGS and WES data from other individuals. In addition to identifying retroCNVs, sideRETRO annotates several characteristics associated with these events. It provides information on the genomic coordinates of the insertion, including chromosome, insertion point, and DNA strand. It also determines the genomic context of the event (exonic, intronic, or intergenic), performs genotyping (presence or absence), and provides haplotyping information (homozygous or heterozygous).

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  dep: libc6 (>= 2.41) [sh4]

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• dep: libhts3t64 (>= 1.17)

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Hämtningar för alla tillgängliga arkitekturer

Arkitektur	Paketstorlek	Installerad storlek	Filer
alpha (inofficiell anpassning)	84,3 kbyte	246,0 kbyte	[filförteckning]
amd64	88,4 kbyte	232,0 kbyte	[filförteckning]
arm64	90,2 kbyte	245,0 kbyte	[filförteckning]
armel	80,8 kbyte	243,0 kbyte	[filförteckning]
armhf	79,4 kbyte	179,0 kbyte	[filförteckning]
i386	93,1 kbyte	247,0 kbyte	[filförteckning]
m68k (inofficiell anpassning)	79,7 kbyte	211,0 kbyte	[filförteckning]
ppc64el	92,5 kbyte	309,0 kbyte	[filförteckning]
riscv64	96,6 kbyte	217,0 kbyte	[filförteckning]
sh4 (inofficiell anpassning)	91,3 kbyte	243,0 kbyte	[filförteckning]
x32 (inofficiell anpassning)	89,2 kbyte	223,0 kbyte	[filförteckning]