SomaMutDB

1. We do not recommend to upload file bigger than 10MB.
2. Hover on the input area for more information.

Example of input files and analyze results

Extract tool:

MutationalPatterns method:

NMF

BayesianNMF

SomaticSignatures Mode:

NMF

PCA

Input file:

Please find the example upload file in the beginning of this page.

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Group file:

Please find the example upload file in the beginning of this page.

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Species name:

human

Genome build:

hg38/GRCh38

hg19/GRCh37

Email:

What to analyse:

analyse SNV
analyse INDEL

Range of signature number to estimate:

Optional parameters:

Analysis samples seperately:

priorSNV (prior mode):

Please find the example upload file in the beginning of this page.

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priorINDEL (prior mode):

Please find the example upload file in the beginning of this page.

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Number of run times:

Use different scale of Y axis:

initcc:

chlist:

burnin:

space:

cpiter:

seed1:

seed2:

matrix of fixed signatures SNV:

Please find the example upload file in the beginning of this page.

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matrix of fixed signatures INDEL:

Please find the example upload file in the beginning of this page.

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nrepeats:

nboots:

clusteringMethod:

matched clustering(MC)

partitioning around the medoids(PAM)

hierarchical clustering(HC)

filterBest_RTOL:

completeLinkageFlag:

useMaxMatching:

filterBestOfEachBootstrap:

filterBest_nmaxtokeep:

mut_thr:

nmfmethod:

brunet

lee

nsNMF

removeDuplicatesInCatalogue:

removeDuplicatesThreshold:

normaliseCatalogue:

nboot for signature fitting:

threshold_percent:

threshold_pvalue:

Method for signature fitting:

KLD

NNLS

bf_method:

KLD

CosSim

alpha:

doRound:

n_sa_iter:

COSMIC version:

Seed file:

Please find the example upload file in the beginning of this page.

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matrix_normalization:

gmm
log2
100X
custom

resample:

nmf init:

random

nndsvd

nndsvda

nndsvdar

nndsvd_min

nmf_replicates:

interation times:

nmf_test_conv:

nmf_tolerance:

nnls_add_penalty:

nnls_remove_penalty:

de_novo_fit_penalty:

initial_remove_penalty:

stability:

min_stability:

combined_stability:

refit_denovo_signatures:

make_decomposition_plots:

get_all_signature_matrices:

precision:

single

double

Exome data:

Signature file 1: Please find the example upload file in the beginning of this page.
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Signature file 2: Please find the example upload file in the beginning of this page.
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Color:
Cluster:
	Cluster rows Cluster columns
Cluster method:
Plot cosine similarity value:
Email:

Fit tool:
MutationalPatterns method:
Input file: Please find the example upload file in the beginning of this page.
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Activities file: Please find the example upload file in the beginning of this page.
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Prior file: Please find the example upload file in the beginning of this page.
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Species name:	human
Genome build:
	hg38/GRCh38 hg19/GRCh37
Email:
What to analyse:
	SNV INDEL
force include:
Optional parameters:
COSMIC version:
signature database file: Please find the example upload file in the beginning of this page.
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nboot:
max_delta:
method:
	strict regular regular_10+
Reducing:
bootstrap:
bootstrap reducing:
iterations:
cos sim threshold:
threshold_percent:
threshold_pvalue:
method:
	KLD NNLS SA
bf_method:
	CosSim KLD
alpha:
doRound:
n_sa_iter:
nnls add penalty:
nnls remove penalty:
de_novo fit penalty:
initial remove penalty:
Refit denovo signatures:
Make decomposition plots:
connected_sigs:

Trace id:

Welcome to SomaMutDB!

A database of somatic mutations in normal human tissues