genometric.mspc.core

Using combined evidence from replicates to evaluate ChIP-seq peaks

Science Score: 54.0%

This score indicates how likely this project is to be science-related based on various indicators:

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CITATION.cff file
Found CITATION.cff file
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codemeta.json file
Found codemeta.json file
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.zenodo.json file
Found .zenodo.json file
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DOI references
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Academic publication links
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Committers with academic emails
1 of 10 committers (10.0%) from academic institutions
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Institutional organization owner
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JOSS paper metadata
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Scientific vocabulary similarity
Low similarity (12.4%) to scientific vocabulary

Keywords

analysis chip-seq enriched-regions genome-analysis mspc next-generation-sequencing ngs-analysis overlapping-peaks peak peaks

Keywords from Contributors

interactive mesh interpretability sequences generic projection optim hacking network-simulation

Last synced: 6 months ago · JSON representation ·

Repository

Using combined evidence from replicates to evaluate ChIP-seq peaks

Basic Info

Host: GitHub
Owner: Genometric
License: gpl-3.0
Language: C#
Default Branch: dev
Homepage: https://genometric.github.io/MSPC/
Size: 21.5 MB

Statistics

Stars: 20
Watchers: 3
Forks: 10
Open Issues: 4
Releases: 20

Topics

analysis chip-seq enriched-regions genome-analysis mspc next-generation-sequencing ngs-analysis overlapping-peaks peak peaks

Created over 8 years ago · Last pushed 7 months ago

Metadata Files

Readme License Citation

README.md

Quick Start | Documentation | Download | Publication

About

The analysis of ChIP-seq samples outputs a number of enriched regions, each indicating a protein-DNA interaction or a specific chromatin modification. Enriched regions (commonly known as "peaks") are called when the read distribution is significantly different from the background and its corresponding significance measure (p-value) is below a user-defined threshold.

When replicate samples are analysed, overlapping enriched regions are expected. This repeated evidence can therefore be used to locally lower the minimum significance required to accept a peak. Here, we propose a method for joint analysis of weak peaks.

Given a set of peaks from (biological or technical) replicates, the method combines the p-values of overlapping enriched regions: users can choose a threshold on the combined significance of overlapping peaks and set a minimum number of replicates where the overlapping peaks should be present. The method allows the "rescue" of weak peaks occuring in more than one replicate and outputs a new set of enriched regions for each replicate.

In general, the method groups enriched regions as background, weak, or stringent based on user-defined weak and stringency thresholds. The method then confirms or discards the weak and stringent enriched regions if their combined stringency is at least as significant as a user-defined threshold. The method then performs a multiple testing correction on confirmed enriched regions at a user-defined false-discovery rate, identifying true-positive and false-positive regions. See the following figure as an example, and you may refer to MSPC publications, slides on slideshare, or documentation page for more details.

Download and Run

MSPC is distributed as a cross-platform console application, a .NET library, and a Bioconductor R package.

Owner

Name: Genometric
Login: Genometric
Kind: organization

Repositories: 17
Profile: https://github.com/Genometric

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Jalili"
  given-names: "Vahid"
  orcid: "https://orcid.org/0000-0003-4986-2157"
title: "MSPC"
version: 5.4.0
doi: 10.1093/bioinformatics/btv293
date-released: 2021-03-18
url: "https://github.com/Genometric/MSPC"
preferred-citation:
  type: article
  authors:
  - family-names: "Jalili"
    given-names: "Vahid"
    orcid: "https://orcid.org/0000-0003-4986-2157"
  - family-names: "Matteucci"
    given-names: "Matteo"
    orcid: "https://orcid.org/0000-0002-8306-6739"
  - family-names: "Masseroli"
    given-names: "Marco"
    orcid: "https://orcid.org/0000-0003-2574-1174"
  - family-names: "Morelli"
    given-names: "Marco"
    orcid: "https://orcid.org/0000-0003-1862-667X"
  doi: "10.1093/bioinformatics/btv293"
  journal: "Bioinformatics"
  month: 9
  start: 2761
  end: 2769
  title: "Using combined evidence from replicates to evaluate ChIP-seq peaks"
  issue: 17
  volume: 31
  year: 2015

GitHub Events

Total

Create event: 12
Release event: 1
Issues event: 1
Watch event: 1
Delete event: 9
Issue comment event: 12
Push event: 20
Pull request event: 26

Last Year

Create event: 12
Release event: 1
Issues event: 1
Watch event: 1
Delete event: 9
Issue comment event: 12
Push event: 20
Pull request event: 26

Committers

Last synced: over 2 years ago

All Time

Total Commits: 1,298
Total Committers: 10
Avg Commits per committer: 129.8
Development Distribution Score (DDS): 0.572

Past Year

Commits: 23
Committers: 2
Avg Commits per committer: 11.5
Development Distribution Score (DDS): 0.478

Top Committers

Name	Email	Commits
VJalili	j**d@g**m	555
Vahid	V****i	399
VJalili	J**d@g**m	275
dependabot[bot]	4****]	20
MeriemBahda	6****a	17
fernandoPalluzzi	5****i	15
Vahid Jalili	j**d@h**m	11
Fernando Palluzzi	f**i@g**m	2
Marzia Angela Cremona	M**a@f**a	2
Marzia Angela Cremona	m**8@p**u	2

Committer Domains (Top 20 + Academic)

psu.edu: 1 fsa.ulaval.ca: 1

Issues and Pull Requests

Last synced: 6 months ago

All Time

Total issues: 25
Total pull requests: 115
Average time to close issues: about 2 months
Average time to close pull requests: 16 days
Total issue authors: 17
Total pull request authors: 4
Average comments per issue: 4.24
Average comments per pull request: 0.8
Merged pull requests: 96
Bot issues: 0
Bot pull requests: 44

Past Year

Issues: 2
Pull requests: 27
Average time to close issues: 5 days
Average time to close pull requests: 2 days
Issue authors: 2
Pull request authors: 2
Average comments per issue: 1.5
Average comments per pull request: 0.48
Merged pull requests: 16
Bot issues: 0
Bot pull requests: 19

View more stats

Top Authors

Issue Authors

juylmin (3)
VJalili (3)
sufyazi (2)
MeriemBahda (2)
AlexBlais74 (2)
nzx9581 (2)
Ollipolli1909 (1)
TheRealQuantumCheese (1)
xiagjt (1)
EvyDuvernois (1)
LaraBM (1)
omorante (1)
danielcgingerich (1)
dependabot[bot] (1)
amateur-boy (1)

Pull Request Authors

VJalili (64)
dependabot[bot] (57)
MeriemBahda (5)
fernandoPalluzzi (2)

Top Labels

Issue Labels

question (10) documentation (5) rmspc (2) bug (2) release (1) dependencies (1) javascript (1) enhancement (1)

Pull Request Labels

dependencies (57) javascript (55) unit test (17) documentation (15) ci-cd (6) bug (5) website (5) rmspc (5) validation (4) CLI (3) mspc-library (3) enhancement (2) code-smell (1) release (1)

Packages

Total packages: 3
Total downloads:
- bioconductor 6,192 total
- nuget 6,523 total

Total dependent packages: 0
(may contain duplicates)
Total dependent repositories: 0
(may contain duplicates)
Total versions: 16
Total maintainers: 2

nuget.org: genometric.mspc.core-v3.0.0rc

Using combined evidence from replicates to evaluate ChIP-seq peaks

Homepage: https://github.com/Genometric/MSPC
License: gpl-3.0
Latest release: 3.0.0
published about 126 years ago

Versions: 1
Dependent Packages: 0
Dependent Repositories: 0

Rankings

Dependent repos count: 12.7%

Average: 16.1%

Dependent packages count: 19.5%

Last synced: 6 months ago

nuget.org: genometric.mspc.core

Using combined evidence from replicates to evaluate ChIP-seq peaks

Homepage: https://genometric.github.io/MSPC/
License: gpl-3.0
Latest release: 6.1.0
published about 1 year ago

Versions: 10
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 6,523 Total

Rankings

Dependent repos count: 12.7%

Average: 18.6%

Dependent packages count: 19.5%

Downloads: 23.5%

Maintainers (1)

Vahid

Last synced: 6 months ago

bioconductor.org: rmspc

Multiple Sample Peak Calling

Homepage: https://genometric.github.io/MSPC/
Documentation: https://bioconductor.org/packages/release/bioc/vignettes/rmspc/inst/doc/rmspc.pdf
License: GPL-3
Latest release: 1.14.0
published 9 months ago

Versions: 5
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 6,192 Total

Rankings

Dependent repos count: 0.0%

Dependent packages count: 0.0%

Average: 30.3%

Downloads: 90.8%

Maintainers (1)

meriembahda@gmail.com

Last synced: 6 months ago

Dependencies

website/package-lock.json npm

1267 dependencies

website/package.json npm

@docusaurus/core ^2.0.0-beta.ff31de0ff
@docusaurus/preset-classic ^2.0.0-beta.ff31de0ff
@docusaurus/theme-search-algolia ^2.0.0-beta.13
classnames ^2.2.6
react ^16.8.4
react-dom ^16.8.4

CLI/CLI.csproj nuget

Genometric.GeUtilities 6.2.0
Microsoft.Extensions.CommandLineUtils 1.1.1
Newtonsoft.Json 13.0.1
log4net 2.0.10

CLI.Tests/CLI.Tests.csproj nuget

xunit.runner.visualstudio 2.4.1 development
Microsoft.NET.Test.Sdk 16.6.1
xunit 2.4.1

Core/Core.csproj nuget

Genometric.GeUtilities 6.2.0
MathNet.Numerics 4.9.1
System.Collections.Immutable 1.7.1

Core.Tests/Core.Tests.csproj nuget

xunit.runner.visualstudio 2.4.1 development
Genometric.GeUtilities 6.2.0
Microsoft.NET.Test.Sdk 16.6.1
xunit 2.4.1

.github/workflows/build.yml actions

actions/checkout v2 composite
actions/setup-dotnet v1.7.2 composite

.github/workflows/codeql-analysis.yml actions

actions/checkout v2 composite
actions/setup-dotnet v1 composite
github/codeql-action/analyze v1 composite
github/codeql-action/autobuild v1 composite
github/codeql-action/init v1 composite

.github/workflows/docs.yml actions

actions/checkout v2 composite
actions/setup-node v1 composite
peaceiris/actions-gh-pages v3 composite

Benchmark/Benchmark.csproj nuget

Genometric.GeUtilities 6.2.0
System.CommandLine 2.0.0-beta4.22272.1