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octopus luntergroup

37

305

mit

19

Bayesian haplotype-based mutation calling

phasing genomics variants haplotypes single-cell bioinformatics variant-calling de-novo-mutation somatic-variants

Created 2015-02-04

5,045 commits to develop branch, last one about a year ago

somaticseq bioinform

53

195

bsd-2-clause

12

An ensemble approach to accurately detect somatic mutations using SomaticSeq

cancer-genomics somatic-variants

Created 2015-04-09

1,842 commits to master branch, last one 11 days ago

neusomatic bioinform

50

168

other

12

NeuSomatic: Deep convolutional neural networks for accurate somatic mutation detection

genomics deep-learning somatic-variants convolutional-neural-networks

Created 2018-08-24

194 commits to master branch, last one 4 years ago

deepsomatic google

16

154

bsd-3-clause

12

DeepSomatic is an analysis pipeline that uses a deep neural network to call somatic variants from tumor-normal and tumor-only sequencing data.

dna genome machine science genomics sequencing deepsomatic deep-learning bioinformatics somatic-variants somatic-mutations

Created 2023-10-11

14 commits to r1.8 branch, last one 22 days ago

SigProfilerExtractor AlexandrovLab

52

154

bsd-2-clause

22

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in e...

bioinformatics cancer-genomics somatic-variants mutation-analysis mutational-signatures

Created 2018-08-30

458 commits to master branch, last one 15 days ago

sigminer ShixiangWang

19

148

other

2

🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html

r cnv dbs nmf sbs indel easy-to-use bayesian-nmf visualization bioinformatics nmf-extraction cancer-research somatic-variants cosmic-signatures somatic-mutations signature-extraction copynumber-signatures mutational-signatures

Created 2018-12-30

1,261 commits to master branch, last one 2 months ago

SigProfilerMatrixGenerator AlexandrovLab

36

101

bsd-2-clause

23

SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file)....

bioinformatics cancer-genomics somatic-variants mutation-analysis mutational-signatures

Created 2018-08-27

312 commits to master branch, last one about a month ago

TCGAmutations PoisonAlien

24

90

mit

5

R data package for pre-compiled somatic mutations from TCGA cohorts and CCLE

maf ccle maftools mutations tcga-data somatic-variants

Created 2017-10-04

20 commits to master branch, last one 2 months ago

Monopogen KChen-lab

18

85

gpl-3.0

3

SNV calling from single cell sequencing

snvs single-cell somatic-variants germline-variants

Created 2022-04-20

316 commits to main branch, last one about a month ago

sv-callers GooglingTheCancerGenome

35

78

apache-2.0

4

Snakemake-based workflow for detecting structural variants in genomic data

wgs workflow snakemake sv-calling bioinformatics cancer-genomics hpc-applications somatic-variants germline-variants structural-variants

Created 2017-04-10

474 commits to master branch, last one 10 months ago

ClairS HKU-BAL

7

78

bsd-3-clause

6

ClairS - a deep-learning method for long-read somatic small variant calling

ont snvs indels pacbio phasing genomics illumina nanopore haplotypes long-reads short-reads deep-learning bioinformatics somatic-variants somatic-mutations long-read-sequencing

Created 2021-07-29

762 commits to main branch, last one 26 days ago

ClairS-TO HKU-BAL

3

54

bsd-3-clause

3

ClairS-TO - a deep-learning method for tumor-only somatic variant calling

ont snvs pacbio tumors genomics illumina nanopore variants long-reads tumor-only deep-learning bioinformatics variant-calling somatic-variants somatic-mutations long-read-sequencing

Created 2023-11-07

163 commits to main branch, last one 23 days ago