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Quick readme update #14

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Quick readme update #14

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# [<img src="https://raw.githubusercontent.com/CCBR/.github/main/img/ccbrbanner.png">](https://bioinformatics.ccr.cancer.gov/ccbr/)
[<img src="https://raw.githubusercontent.com/CCBR/.github/main/img/ccbrbanner.png">](https://bioinformatics.ccr.cancer.gov/ccbr/)
## Table of Contents

- [NEW Releases](#new-releases)
- [TOP contributors](#top-contributors)
- [About Us](#about-us)
- [Our model](#our-model)
- [Pipelines](#pipelines)
- [Tools](#tools)
- [Release History](#release-history)
- [Latest Releases of pipelines/tools:](#latest-releases-of-pipelines/tools:)
- [Citation](#citation)

## NEW Releases

| Repo Name | Release Name | Release Date | Open Issues |
|:-----------------------------------------------------|:---------------------------------------------------------------------------|:---------------|--------------:|
| [spacesavers2](https://github.com/CCBR/spacesavers2) | [v0.14.0](https://github.com/CCBR/spacesavers2/releases/tag/v0.14.0) | 2024-07-16 | 5 |
| [XAVIER](https://github.com/CCBR/XAVIER) | [v3.0.3](https://github.com/CCBR/XAVIER/releases/tag/v3.0.3) | 2024-07-11 | 9 |
| [ESCAPE](https://github.com/CCBR/ESCAPE) | [v1.1.2](https://github.com/CCBR/ESCAPE/releases/tag/v1.1.2) | 2024-06-27 | 1 |
| [permfix](https://github.com/CCBR/permfix) | [v0.6.4](https://github.com/CCBR/permfix/releases/tag/v0.6.4) | 2024-05-07 | 0 |
| [journal-club](https://github.com/CCBR/journal-club) | [jchelper 0.1.0](https://github.com/CCBR/journal-club/releases/tag/v0.1.0) | 2024-05-07 | 2 |
| [reports](https://github.com/CCBR/reports) | [ccbr.reports 0.2.0](https://github.com/CCBR/reports/releases/tag/v0.2.0) | 2024-04-30 | 11 |

## TOP contributors

| User | Total Commits | Commits in Last Month | Commits in Last 6 Months |
|:---------------|----------------:|------------------------:|---------------------------:|
| kopardev | 4114 | 31 | 528 |
| kelly-sovacool | 3310 | 122 | 1051 |
| slsevilla | 1700 | 0 | 119 |
| skchronicles | 1074 | 0 | 0 |
| dnousome | 647 | 13 | 137 |
| kcgfarb | 478 | 28 | 169 |
| finneyr | 342 | 1 | 20 |
| samarth8392 | 339 | 20 | 99 |
| jlac | 307 | 0 | 0 |
| kvaldez | 222 | 0 | 0 |

## About Us

### About Us
- 👋 Hi, we're the [**@CCBR**](https://bioinformatics.ccr.cancer.gov/ccbr/), a group of bioinformatics analysts and engineers
- 📖 We build flexible, reproducible, workflows for next-generation sequencing data
- :bulb: We [collaborate](https://abcs-amp.nih.gov/project/request/CCBR/) with [CCR](https://ccr.cancer.gov/) PIs
- 📫 You can reach us at [[email protected]](mailto:[email protected])
- 🏁 Check out our [release history](#release-history)
- :link: Our [Zenodo](https://zenodo.org/communities/ccbr) community
<hr>
<p align="center">
<a href="##table-of-contents">Back to Top</a>
</p>

### Our model
## Our model

[<img src="https://raw.githubusercontent.com/CCBR/.github/main/img/CCBR_circle_diagram.png" width=600>](https://bioinformatics.ccr.cancer.gov/ccbr/)

### Pipelines
<hr>
<p align="center">
<a href="##table-of-contents">Back to Top</a>
</p>

## Pipelines

CCBR offers end-to-end analysis pipelines for NGS data analysis.

Expand All @@ -28,11 +75,13 @@ Here is a list of our prominent pipelines and their release schedule on BIOWULF:
| WESSeq<sup>2</sup> | [XAVIER](https://github.com/CCBR/XAVIER)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | July 21th 2023 | Sep 1st 2023 |
| ATACSeq<sup>3</sup> | [ASPEN](https://github.com/CCBR/ASPEN)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | November 30th 2023 | TBD |
| ChIPSeq<sup>4</sup> | [CHAMPAGNE](https://github.com/CCBR/CHAMPAGNE)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | October 15th 2023 | TBD |
| CRISPRSeq<sup>5</sup> | [CRUISE](https://github.com/CCBR/CRUISE)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | October 31st 2023 | TBD |
| CRISPRSeq<sup>5</sup> | [CRISPIN](https://github.com/CCBR/CRISPIN)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | September 31st 2023 | TBD |
| CUT&RunSeq<sup>6</sup> | [CARLISLE](https://github.com/CCBR/CARLISLE)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | October 31st 2023 | TBD |
| circRNASeq<sup>7</sup> | [CHARLIE](https://github.com/CCBR/CHARLIE)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | March 31st 2024 | TBD |
| scRNASeq<sup>8</sup> | [SINCLAIR](https://github.com/CCBR/SINCLAIR)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | April 30th 2024 | TBD |
| WGSSeq<sup>9</sup> | [LOGAN](https://github.com/CCBR/LOGAN)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | May 31st 2024 | TBD |
| EV-Seq<sup>10</sup> | [ESCAPE](https://github.com/CCBR/ESCAPE)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | March 26th, 2024 | TBD |
| circRNASeq<sup>7</sup> | [CHARLIE](https://github.com/CCBR/CHARLIE)![snakemake](https://raw.githubusercontent.com/CCBR/.github/main/img/snakemake-small-v2.svg) | _Jul 31st 2024_ | TBD |
| scRNASeq<sup>8</sup> | [SINCLAIR](https://github.com/CCBR/SINCLAIR)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | _Sep 30th 2024_ | TBD |
| WGSSeq<sup>9</sup> | [LOGAN](https://github.com/CCBR/LOGAN)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | _Sep 30th 2024_ | TBD |
| spatialSeq<sup>11</sup> | [SPENCER](https://github.com/CCBR/SPENCER)![nextflow](https://raw.githubusercontent.com/CCBR/.github/main/img/nextflow-small-v2.svg) | TBD | TBD |

<sup>* CLI = Command Line Interface </sup>
<sup>* GUI = Graphical User Interface </sup>
Expand All @@ -53,16 +102,20 @@ Here is a list of our prominent pipelines and their release schedule on BIOWULF:

<sup> **8** SINCLAIR=_SINgle CelL AnalysIs Resource_ addresses various single cell modalities... eg. single-cell expression, CITESeq, TCR-Seq, etc.</sup>

<sup> **9** WGSSeq pipeline will soon be CCBR's newest offering.</sup>
<sup> **9** LOGAN=_whoLe genOme-sequencinG Analysis pipeliNe_ will soon be CCBR's newest offering.</sup>

<sup> **10** ESCAPE=_Extracellular veSiCles rnAseq PipelinE_.</sup>

<sup> **11** SPENCER=_SPatial seqeENCing Resource_.</sup>

For any other datatype or pipeline, please [email :mailbox:](mailto:[email protected]) us directly to get the conversation started!

<hr>
<p align="center">
<a href="##ccr-collaborative-bioinformatics-resource">Back to Top</a>
<a href="##table-of-contents">Back to Top</a>
</p>

### Tools
## Tools

In additions to end-to-end analysis pipelines, the CCBR dev team also builds tools for data management, meta-data management, APIs, user management, etc. Here are some examples:

Expand All @@ -72,10 +125,10 @@ In additions to end-to-end analysis pipelines, the CCBR dev team also builds too

<hr>
<p align="center">
<a href="##ccr-collaborative-bioinformatics-resource">Back to Top</a>
<a href="##table-of-contents">Back to Top</a>
</p>

### Release History
## Release History

`module load ccbrpipeliner` loads default release of ccbrpipeliner. Each release comprises of a unique combination of the version numbers of the different pipelines offered as part of the ccbrpipeliner suite.

Expand All @@ -94,12 +147,57 @@ In additions to end-to-end analysis pipelines, the CCBR dev team also builds too
> <sup>@</sup> = CLI available
>
> <sup>#</sup> = GUI available
<hr>
<p align="center">
<a href="##table-of-contents">Back to Top</a>
</p>
## Latest Releases of pipelines/tools:

| Repo Name | Release Name | Release Date | Open Issues |
|:-------------------------------------------------------------------------------------------------------------------------|:----------------------------------------------------------------------------------------------------------------|:---------------|--------------:|
| [spacesavers2](https://github.com/CCBR/spacesavers2) | [v0.14.0](https://github.com/CCBR/spacesavers2/releases/tag/v0.14.0) | 2024-07-16 | 5 |
| [XAVIER](https://github.com/CCBR/XAVIER) | [v3.0.3](https://github.com/CCBR/XAVIER/releases/tag/v3.0.3) | 2024-07-11 | 9 |
| [ESCAPE](https://github.com/CCBR/ESCAPE) | [v1.1.2](https://github.com/CCBR/ESCAPE/releases/tag/v1.1.2) | 2024-06-27 | 1 |
| [permfix](https://github.com/CCBR/permfix) | [v0.6.4](https://github.com/CCBR/permfix/releases/tag/v0.6.4) | 2024-05-07 | 0 |
| [journal-club](https://github.com/CCBR/journal-club) | [jchelper 0.1.0](https://github.com/CCBR/journal-club/releases/tag/v0.1.0) | 2024-05-07 | 2 |
| [reports](https://github.com/CCBR/reports) | [ccbr.reports 0.2.0](https://github.com/CCBR/reports/releases/tag/v0.2.0) | 2024-04-30 | 11 |
| [parkit](https://github.com/CCBR/parkit) | [v2.0.1](https://github.com/CCBR/parkit/releases/tag/v2.0.1) | 2024-04-16 | 0 |
| [CCBR_tobias](https://github.com/CCBR/CCBR_tobias) | [CCBR_tobias 0.3.0](https://github.com/CCBR/CCBR_tobias/releases/tag/v0.3.0) | 2024-04-12 | 1 |
| [RENEE](https://github.com/CCBR/RENEE) | [RENEE 2.5.12](https://github.com/CCBR/RENEE/releases/tag/v2.5.12) | 2024-04-12 | 22 |
| [METRO](https://github.com/CCBR/METRO) | [v2.1](https://github.com/CCBR/METRO/releases/tag/v2.1) | 2024-03-28 | 2 |
| [CCBR-1144](https://github.com/CCBR/CCBR-1144) | [Data Release Latest](https://github.com/CCBR/CCBR-1144/releases/tag/v1.0.0) | 2024-03-04 | 0 |
| [CARLISLE](https://github.com/CCBR/CARLISLE) | [v2.5.0](https://github.com/CCBR/CARLISLE/releases/tag/v.2.5.0) | 2024-02-26 | 13 |
| [TRANQUIL](https://github.com/CCBR/TRANQUIL) | [TRANQUIL 0.2.1](https://github.com/CCBR/TRANQUIL/releases/tag/v0.2.1) | 2024-02-22 | 0 |
| [ccbr1271_ERVpipeline](https://github.com/CCBR/ccbr1271_ERVpipeline) | [v1.0.3](https://github.com/CCBR/ccbr1271_ERVpipeline/releases/tag/v1.0.3) | 2024-02-21 | 1 |
| [nf-sandbox](https://github.com/CCBR/nf-sandbox) | [nf-sandbox 0.2.1](https://github.com/CCBR/nf-sandbox/releases/tag/v0.2.1) | 2024-01-26 | 3 |
| [CHAMPAGNE](https://github.com/CCBR/CHAMPAGNE) | [CHAMPAGNE 0.3.0](https://github.com/CCBR/CHAMPAGNE/releases/tag/v0.3.0) | 2024-01-18 | 30 |
| [ASPEN](https://github.com/CCBR/ASPEN) | [v1.0.1](https://github.com/CCBR/ASPEN/releases/tag/v1.0.1) | 2023-12-27 | 6 |
| [CHARLIE](https://github.com/CCBR/CHARLIE) | [v0.10.1](https://github.com/CCBR/CHARLIE/releases/tag/v0.10.1) | 2023-12-23 | 20 |
| [nf-modules](https://github.com/CCBR/nf-modules) | [nf-modules 0.1.0](https://github.com/CCBR/nf-modules/releases/tag/v0.1.0) | 2023-11-29 | 11 |
| [CRISPIN](https://github.com/CCBR/CRISPIN) | [CRUISE 0.1.1](https://github.com/CCBR/CRISPIN/releases/tag/v0.1.1) | 2023-11-06 | 14 |
| [SINCLAIR](https://github.com/CCBR/SINCLAIR) | [v0.2.0](https://github.com/CCBR/SINCLAIR/releases/tag/v0.2.0) | 2023-11-01 | 26 |
| [CRISPRAnnotation](https://github.com/CCBR/CRISPRAnnotation) | [Code/Data Release](https://github.com/CCBR/CRISPRAnnotation/releases/tag/v1.0) | 2023-10-19 | 0 |
| [SharanLab](https://github.com/CCBR/SharanLab) | [Data/Code Release](https://github.com/CCBR/SharanLab/releases/tag/v1.0.0) | 2023-07-18 | 0 |
| [Pipeliner](https://github.com/CCBR/Pipeliner) | [v4.0.7](https://github.com/CCBR/Pipeliner/releases/tag/v4.0.7) | 2023-05-09 | 24 |
| [MAPLE](https://github.com/CCBR/MAPLE) | [version 1.0.1](https://github.com/CCBR/MAPLE/releases/tag/v1.0.1) | 2023-02-27 | 0 |
| [DTB_ExomeSeq](https://github.com/CCBR/DTB_ExomeSeq) | [v1.0](https://github.com/CCBR/DTB_ExomeSeq/releases/tag/v1.0) | 2022-06-22 | 0 |
| [ASCENT](https://github.com/CCBR/ASCENT) | [v0.1.1](https://github.com/CCBR/ASCENT/releases/tag/v0.1.1) | 2022-01-04 | 2 |
| [Antitumor-activity-of-entinostat-plus-NHS-IL12](https://github.com/CCBR/Antitumor-activity-of-entinostat-plus-NHS-IL12) | [Manuscript Methods](https://github.com/CCBR/Antitumor-activity-of-entinostat-plus-NHS-IL12/releases/tag/v.1.0) | 2021-06-01 | 0 |
| [CCBR_circRNA_AmpliconSeq](https://github.com/CCBR/CCBR_circRNA_AmpliconSeq) | [v0.1.1](https://github.com/CCBR/CCBR_circRNA_AmpliconSeq/releases/tag/v0.1.1) | 2021-03-24 | 0 |
| [rNA](https://github.com/CCBR/rNA) | [Release v1.0.0](https://github.com/CCBR/rNA/releases/tag/v1.0.0) | 2021-01-21 | 0 |
| [l2p](https://github.com/CCBR/l2p) | [Release v0.0.3](https://github.com/CCBR/l2p/releases/tag/v0.0.3) | 2020-07-13 | 0 |
| [MAAPster](https://github.com/CCBR/MAAPster) | [Release v2.0.0](https://github.com/CCBR/MAAPster/releases/tag/v2.0.0) | 2020-04-27 | 0 |
| [ChIP-Seq-Pipeline](https://github.com/CCBR/ChIP-Seq-Pipeline) | [Alpha 2](https://github.com/CCBR/ChIP-Seq-Pipeline/releases/tag/alpha2) | 2016-10-01 | 2 |

<hr>
<p align="center">
<a href="##ccr-collaborative-bioinformatics-resource">Back to Top</a>
<a href="##table-of-contents">Back to Top</a>
</p>

### Citation
## Citation

Most of our end-to-end pipelines which have been used in published research work have been made available to the entire bioinformatics community via a Zenodo DOI. Please feel free to visit our [Zenodo community page](https://zenodo.org/communities/ccbr). And if you use our pipelines, don't forget to cite us!
<hr>
<p align="center">
<a href="##table-of-contents">Back to Top</a>
</p>
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