hermes

Preprocessing, analyzing, and reporting of RNA-seq data

https://github.com/insightsengineering/hermes

Science Score: 26.0%

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

○
CITATION.cff file
✓
codemeta.json file
Found codemeta.json file
✓
.zenodo.json file
Found .zenodo.json file
○
DOI references
○
Academic publication links
○
Committers with academic emails
○
Institutional organization owner
○
JOSS paper metadata
○
Scientific vocabulary similarity
Low similarity (16.9%) to scientific vocabulary

Keywords

r r-package rna-seq rstats statistical-engineering

Last synced: 9 months ago · JSON representation

Repository

Preprocessing, analyzing, and reporting of RNA-seq data

Basic Info

Host: GitHub
Owner: insightsengineering
Language: R
Default Branch: main
Homepage: https://insightsengineering.github.io/hermes/
Size: 54 MB

Statistics

Stars: 12
Watchers: 21
Forks: 2
Open Issues: 5
Releases: 5

Topics

r r-package rna-seq rstats statistical-engineering

Created almost 5 years ago · Last pushed 9 months ago

Metadata Files

Readme Changelog Contributing

README.Rmd

---
output: github_document
---



# hermes   

```{r, echo = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>",
  fig.path = "README-"
)
```


[![Check 🛠](https://github.com/insightsengineering/hermes/actions/workflows/check.yaml/badge.svg)](https://github.com/insightsengineering/hermes/actions/workflows/check.yaml)
[![Docs 📚](https://github.com/insightsengineering/hermes/actions/workflows/docs.yaml/badge.svg)](https://insightsengineering.github.io/hermes/)
[![Code Coverage 📔](https://raw.githubusercontent.com/insightsengineering/hermes/_xml_coverage_reports/data/main/badge.svg)](https://raw.githubusercontent.com/insightsengineering/hermes/_xml_coverage_reports/data/main/coverage.xml)

![GitHub forks](https://img.shields.io/github/forks/insightsengineering/hermes?style=social)
![GitHub repo stars](https://img.shields.io/github/stars/insightsengineering/hermes?style=social)

![GitHub commit activity](https://img.shields.io/github/commit-activity/m/insightsengineering/hermes)
![GitHub contributors](https://img.shields.io/github/contributors/insightsengineering/hermes)
![GitHub last commit](https://img.shields.io/github/last-commit/insightsengineering/hermes)
![GitHub pull requests](https://img.shields.io/github/issues-pr/insightsengineering/hermes)
![GitHub repo size](https://img.shields.io/github/repo-size/insightsengineering/hermes)
![GitHub language count](https://img.shields.io/github/languages/count/insightsengineering/hermes)
[![Project Status: Active – The project has reached a stable, usable state and is being actively developed.](https://www.repostatus.org/badges/latest/active.svg)](https://www.repostatus.org/#active)
[![Current Version](https://img.shields.io/github/r-package/v/insightsengineering/hermes/main?color=purple\&label=package%20version)](https://github.com/insightsengineering/hermes/tree/main)
[![Open Issues](https://img.shields.io/github/issues-raw/insightsengineering/hermes?color=red\&label=open%20issues)](https://github.com/insightsengineering/hermes/issues?q=is%3Aissue+is%3Aopen+sort%3Aupdated-desc)

\

> `hermes` facilitates preprocessing, analyzing, and reporting of RNA-seq data.

- Imports `RNAseq` count data into the `hermes` ready format.
- Annotates gene information automatically from a central database (e.g. `BioMart`).
- Adds quality control (QC) flags to genes and samples.
- Filters the data set.
- Normalizes the counts.
- Quickly produces descriptive plots.
- Performs principal components analysis.
- Produces a templated QC report.
- Performs differential expression analysis.

## Installation

### `BioConductor`

You can install the current release from `BioConductor` with:

```{r bioc-installation, eval = FALSE}
if (!require("BiocManager")) {
  install.packages("BiocManager")
}
BiocManager::install("hermes")
```

### GitHub

You can install the development version from GitHub with:

```{r gh-installation, eval = FALSE}
if (!require("devtools")) {
  install.packages("devtools")
}
devtools::install_github("insightsengineering/hermes")
```

## Getting Started

You can get started by reading the introduction vignette:

```{r vignette-start, eval = FALSE}
library(hermes)
vignette("introduction", package = "hermes")
```

Owner

Name: Roche/Genentech - Insights Engineering
Login: insightsengineering
Kind: organization
Location: Switzerland

Website: https://code4life.roche.com/
Repositories: 53
Profile: https://github.com/insightsengineering

Roche/Genentech - Insights Engineering

GitHub Events

Total

Watch event: 2
Delete event: 7
Issue comment event: 24
Push event: 63
Pull request review comment event: 4
Pull request review event: 10
Pull request event: 7
Create event: 6

Last Year

Watch event: 2
Delete event: 7
Issue comment event: 24
Push event: 63
Pull request review comment event: 4
Pull request review event: 10
Pull request event: 7
Create event: 6

Committers

Last synced: over 2 years ago

All Time

Total Commits: 562
Total Committers: 42
Avg Commits per committer: 13.381
Development Distribution Score (DDS): 0.699

Past Year

Commits: 33
Committers: 9
Avg Commits per committer: 3.667
Development Distribution Score (DDS): 0.576

Top Committers

Name	Email	Commits
Daniel Sabanes Bove	d**e@r**m	169
Daniel Sabanes Bove	d****e	47
Jeff Luong	j**g@r**m	47
Stefanie	s**1@r**m	45
Simona Rossomanno	s**o@r**m	41
Namrata Bhatia	b**3@g**m	33
Haocheng	h**i@r**m	21
Dinakar	2****9	19
Insights Engineering Bot	6****t	15
walkowif	5****f	14
arkadiuszbeer	8****r	11
Lyndsee Z	z**8@g**m	10
Dave	1****e	10
Zhang, Lyndsee Midori {MDBN~South San Francisco}	z**e@g**m	8
Bhatia, Namrata {MDBN~South San Francisco}	b**a@g**m	6
colinisstudent	8****t	6
Nikolas Burkoff	n**f@r**m	5
Pawel Rucki	p**i@g**m	4
b_falquet	6****t	4
Konrad Pagacz	k**z@c**m	4
namratabhatia	5****a	4
Pawel Rucki	p**i@r**m	3
J Zhao	j**5@g**m	3
Tim Treis	t**s@r**m	3
Jeff Luong	8****3	3
Stefanie Bienert	7****s	3
pawelru	p****u	3
Mahmoud Hallal	8****1	2
cicdguy	c****y	2
alexjoerich	7****h	2
and 12 more...

Committer Domains (Top 20 + Academic)

roche.com: 10 gene.com: 4 waddell.ch: 1 tessella.com: 1 cybertronika.eu: 1 contractors.roche.com: 1

Issues and Pull Requests

Last synced: 9 months ago

All Time

Total issues: 22
Total pull requests: 89
Average time to close issues: about 1 month
Average time to close pull requests: 4 days
Total issue authors: 5
Total pull request authors: 19
Average comments per issue: 0.91
Average comments per pull request: 2.97
Merged pull requests: 78
Bot issues: 0
Bot pull requests: 0

Past Year

Issues: 0
Pull requests: 6
Average time to close issues: N/A
Average time to close pull requests: 3 days
Issue authors: 0
Pull request authors: 3
Average comments per issue: 0
Average comments per pull request: 4.83
Merged pull requests: 3
Bot issues: 0
Bot pull requests: 0

View more stats

Top Authors

Issue Authors

danielinteractive (15)
pawelru (3)
cicdguy (2)
nikolas-burkoff (1)
BFalquet (1)

Pull Request Authors

danielinteractive (19)
walkowif (13)
insights-engineering-bot (10)
arkadiuszbeer (6)
m7pr (5)
BFalquet (5)
vedhav (4)
pawelru (4)
knightdave (4)
cicdguy (4)
tomszosz (2)
kpagacz (2)
nikolas-burkoff (2)
alexjoerich (2)
denisovan31415 (2)

Top Labels

Issue Labels

bug (8) devops (6) SP1 (5) SP3 (3) SP2 (3) biomarker (2) documentation (2) good first issue (2) core (1) enhancement (1) SP5 (1) priority (1)

Pull Request Labels

core (16) automation (6) biomarker (4) documentation (2) bug (2) blocked (1) devops (1)

Packages

Total packages: 1
Total downloads:
- bioconductor 10,136 total

Total dependent packages: 0
Total dependent repositories: 0
Total versions: 7
Total maintainers: 1

bioconductor.org: hermes

Preprocessing, analyzing, and reporting of RNA-seq data

Homepage: https://github.com/insightsengineering/hermes/
Documentation: https://bioconductor.org/packages/release/bioc/vignettes/hermes/inst/doc/hermes.pdf
License: Apache License 2.0
Latest release: 1.12.1
published about 1 year ago

Versions: 7
Dependent Packages: 0
Dependent Repositories: 0
Downloads: 10,136 Total

Rankings

Dependent repos count: 0.0%

Dependent packages count: 0.0%

Average: 28.9%

Downloads: 86.8%

Maintainers (1)

daniel.sabanes_bove@rconis.com

Last synced: 9 months ago

Dependencies

DESCRIPTION cran

R >= 3.5 depends
SummarizedExperiment >= 1.16 depends
ggfortify * depends
Biobase * imports
BiocGenerics * imports
ComplexHeatmap * imports
DESeq2 * imports
EnvStats * imports
GenomicRanges * imports
IRanges * imports
MultiAssayExperiment * imports
R6 * imports
Rdpack * imports
S4Vectors * imports
assertthat * imports
biomaRt * imports
checkmate >= 2.1 imports
circlize * imports
dplyr * imports
edgeR * imports
forcats * imports
ggplot2 * imports
ggrepel >= 0.9 imports
lifecycle * imports
limma * imports
magrittr * imports
matrixStats * imports
methods * imports
purrr * imports
rlang * imports
stats * imports
tidyr * imports
utils * imports
BiocStyle * suggests
DT * suggests
DelayedArray * suggests
grid * suggests
httr * suggests
knitr * suggests
rmarkdown * suggests
statmod * suggests
testthat >= 2.0 suggests
vdiffr * suggests

.github/workflows/check.yaml actions

.github/workflows/docs.yaml actions

.github/workflows/post-release.yaml actions

.github/workflows/release.yaml actions

ecosyste.ms

Data

Tools

Indexes

Applications

Experiments

Open Source Science

hermes

Science Score: 26.0%

Keywords

Repository

Basic Info

Statistics

Topics

Metadata Files

README.Rmd

Owner

GitHub Events

Total

Last Year

Committers

All Time

Past Year

Top Committers

Committer Domains (Top 20 + Academic)

Issues and Pull Requests

All Time

Past Year

Top Authors

Issue Authors

Pull Request Authors

Top Labels

Issue Labels

Pull Request Labels

Packages

bioconductor.org: hermes

Rankings

Maintainers (1)

Dependencies