qpcr-pipeline

Auto-analysis for Real-Time PCR (qPCR) data

https://github.com/tiramisutes/qpcr-pipeline

Science Score: 44.0%

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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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Scientific vocabulary similarity
Low similarity (8.2%) to scientific vocabulary

Keywords

python qpcr r

Last synced: 6 months ago · JSON representation ·

Repository

Auto-analysis for Real-Time PCR (qPCR) data

Basic Info

Host: GitHub
Owner: tiramisutes
License: apache-2.0
Language: R
Default Branch: master
Homepage: https://ihope.shinyapps.io/qRT-PCR-Pipeline/
Size: 101 KB

Statistics

Stars: 37
Watchers: 1
Forks: 16
Open Issues: 0
Releases: 0

Topics

python qpcr r

Created about 7 years ago · Last pushed over 2 years ago

Metadata Files

Readme License Citation

Real-Time PCR (qPCR) Pipeline

Auto-analysis for Real-Time PCR (qPCR) data.

This qPCR experiment usually have two group: Control (CK) and sample, and at least two type genes: Housekeeping Gene (HG) and Target Gene (TG). In our lab this usually label with ub7 and ve.

Congratulations! A alternative way to analysis of qPCR data can be find in : A shiny for analysis qRT-PCR data

Dependencies
INPUT
USAGE
OUTPUT ## 1. Dependencies
python
- collections
- itertools
- csv
- pandas
- numpy
- sys
R
- ggplot2
- gridExtra
- ggthemes
- ggsci
- reshape2
- dplyr ## 2. INPUT There is a example input data in Example_data/. ## 3. USAGE ./qPCR.sh A B C D E F Argument:
A: absolute path of Input data (e, /public/home/hope/qPCR)
B: Input Data (e, rawinputqPCR.csv)
C: Width of output pdf file
D: Height of output pdf file
E: Whether plot a scientific journals figure using the ggsci packages (yes or no)
F: The sample name used as reference level in ANOVA analysis

Running on the example data: ./qPCR.sh /public/home/hope/qPCR raw_input_qPCR.csv 18 8 no CK

4. OUTPUT

rawinputqPCR_ubq7.csv
rawinputqPCR_ve.csv
RQrawinputqPCR_ve.csv
RQrawinputqPCR_ubq7.csv
rawinputqPCR_R.csv
rawinputqPCR_ANOVA.csv
ProrawinputqPCRR.csv
Prorawinput_qPCR.pdf
rawinputqPCR_T-test.pdf

Owner

Name: hope
Login: tiramisutes
Kind: user

Website: http://tiramisutes.github.io/
Twitter: hopetogy
Repositories: 1
Profile: https://github.com/tiramisutes

Bioinformatician, interested in genomics.

Citation (CITATION.cff)

cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Lisa"
  given-names: "Mona"
  orcid: "https://orcid.org/0000-0000-0000-0000"
- family-names: "Bot"
  given-names: "Hew"
  orcid: "https://orcid.org/0000-0000-0000-0000"
title: "My Research Software"
version: 2.0.4
doi: 10.5281/zenodo.1234
date-released: 2017-12-18
url: "https://github.com/github/linguist"
preferred-citation:
  type: article
  authors:
  - family-names: "Lisa"
    given-names: "Mona"
    orcid: "https://orcid.org/0000-0000-0000-0000"
  - family-names: "Bot"
    given-names: "Hew"
    orcid: "https://orcid.org/0000-0000-0000-0000"
  doi: "10.0000/00000"
  journal: "Journal Title"
  month: 9
  start: 1 # First page number
  end: 10 # Last page number
  title: "My awesome research software"
  issue: 1
  volume: 1
  year: 2021

GitHub Events

Total

Watch event: 2
Fork event: 1

Last Year

Watch event: 2
Fork event: 1

Committers

Last synced: over 2 years ago

All Time

Total Commits: 70
Total Committers: 1
Avg Commits per committer: 70.0
Development Distribution Score (DDS): 0.0

Past Year

Commits: 11
Committers: 1
Avg Commits per committer: 11.0
Development Distribution Score (DDS): 0.0

Top Committers

Name	Email	Commits
hope	1**8@q**m	70

Committer Domains (Top 20 + Academic)

qq.com: 1

ecosyste.ms

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