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FLAMES

A framework for performing single-cell and bulk read full-length analysis of mutations and splicing.

https://github.com/mritchielab/flames

Science Score: 26.0%

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Repository

A framework for performing single-cell and bulk read full-length analysis of mutations and splicing.

Basic Info
Statistics
  • Stars: 39
  • Watchers: 3
  • Forks: 12
  • Open Issues: 9
  • Releases: 0
Created over 5 years ago · Last pushed 10 months ago
Metadata Files
Readme Changelog Contributing License Code of conduct

README.md

FLAMES

R build status

The FLAMES package provides a framework for performing single-cell and bulk read full-length analysis of mutations and splicing. FLAMES performs cell barcode and UMI assignment from nanopore reads as well as semi-supervised isoform detection and quantification. FLAMES is designed to be an easy and quick to use, powerful workflow for isoform detection and quantification, splicing analysis and mutation detection.

Input to FLAMES are fastq files generated from the long-read platform. Using the cell barcode annotation obtained from short-read data as the reference, the pipeline identifies and trims cell barcodes/UMI sequences from the long reads. After barcode assignment, all reads are aligned to the relevant genome to obtain a draft read alignment. The draft alignment is then polished and grouped to generate a consensus transcript assembly. All reads are aligned again using the transcript assembly as the reference and quantified.

The above figure provides a high level overview of the main steps in the FLAMES pipeline. The optional arguments on the left are colour coded to associate with the specific step that they apply to.

Installation

The Bioconductor release of FLAMES can be installed with: ``` if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")

BiocManager::install("FLAMES") ```

The latest development version can be installed with: if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager") BiocManager::install("mritchielab/FLAMES")

⚠️ Installing source packages inside a conda environment might cause various issues

Please consider using Docker or Singularity instead if you cannot install FLAMES in your native R environment.

Docker

``` docker pull ghcr.io/mritchielab/flames:20af1ce

To start an R session:

docker run -it ghcr.io/mritchielab/flames:20af1ce

Or a bash session:

docker run -it ghcr.io/mritchielab/flames:20af1ce /bin/bash ```

Singularity

singularity pull flames.sif docker://ghcr.io/mritchielab/flames:20af1ce singularity shell -e --writable-tmpfs flames.sif

Documentation

Function reference manual can be found here.

IgniteRNAseq is a workflow package and its rendered vignette can be found here.

A Long read single cell analysis tutorial using both single-sample and multi-sample modes is available here.

Common issues

  • basilisk / reticulate errors
    If you encounter errors from Python code execution, you could try adding basilisk::setBasiliskFork(FALSE) before running FLAMES.

  • Isoform identification with bambu If you encounter errors during isoform identification using Bambu, you can try troubleshooting by setting the '''bambu_verbose''' parameter to TRUE. We have found the following steps helpful in resolving issues:

  1. Remove supplementary alignments from the genome BAM file.

  2. Divide the BAM file into smaller sections for easier processing.

  3. Remove unnecessary contigs from the genome.fa file.

  4. Use the HongYhongfix branch of Bambu, which is better equipped for handling large files. You can install this version in R with the following command: ``` installgithub("GoekeLab/bambu", ref="HongYhong_fix") ```

Owner

  • Name: mritchielab
  • Login: mritchielab
  • Kind: organization

GitHub Events

Total
  • Issues event: 24
  • Watch event: 19
  • Delete event: 1
  • Issue comment event: 41
  • Push event: 89
  • Pull request event: 4
  • Fork event: 3
  • Create event: 2
Last Year
  • Issues event: 24
  • Watch event: 19
  • Delete event: 1
  • Issue comment event: 41
  • Push event: 89
  • Pull request event: 4
  • Fork event: 3
  • Create event: 2

Issues and Pull Requests

Last synced: 10 months ago

All Time
  • Total issues: 52
  • Total pull requests: 19
  • Average time to close issues: 3 months
  • Average time to close pull requests: 25 days
  • Total issue authors: 33
  • Total pull request authors: 8
  • Average comments per issue: 2.38
  • Average comments per pull request: 0.37
  • Merged pull requests: 17
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 18
  • Pull requests: 6
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 3 days
  • Issue authors: 13
  • Pull request authors: 3
  • Average comments per issue: 2.0
  • Average comments per pull request: 0.33
  • Merged pull requests: 4
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • nick-youngblut (9)
  • sparthib (5)
  • vasikara17 (2)
  • brilliantlee2 (2)
  • HenriettaHolze (2)
  • m-noonan (2)
  • nci-tech (2)
  • vsuppiyar (2)
  • mcortes-lopez (2)
  • jadedavis5 (1)
  • vjcitn (1)
  • youyupei (1)
  • maxim-h (1)
  • brianFSM (1)
  • beeesal (1)
Pull Request Authors
  • OliverVoogd (4)
  • LuyiTian (3)
  • felixradtke (2)
  • ChangqingW (2)
  • chingyinwan (2)
  • Sefi196 (2)
  • maxim-h (2)
  • hpages (2)
Top Labels
Issue Labels
bug (4) enhancement (2) question (2) documentation (2)
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • bioconductor 11,368 total
  • Total dependent packages: 0
  • Total dependent repositories: 0
  • Total versions: 7
  • Total maintainers: 1
bioconductor.org: FLAMES

FLAMES: Full Length Analysis of Mutations and Splicing in long read RNA-seq data

  • Versions: 7
  • Dependent Packages: 0
  • Dependent Repositories: 0
  • Downloads: 11,368 Total
Rankings
Dependent repos count: 0.0%
Dependent packages count: 0.0%
Average: 26.4%
Downloads: 79.3%
Maintainers (1)
wang.ch@wehi.edu.au
Last synced: 10 months ago

Dependencies

DESCRIPTION cran
  • BiocGenerics * imports
  • Biostrings * imports
  • ComplexHeatmap * imports
  • GenomeInfoDb * imports
  • GenomicFeatures * imports
  • GenomicRanges * imports
  • Matrix * imports
  • RColorBrewer * imports
  • Rsamtools * imports
  • S4Vectors * imports
  • SingleCellExperiment * imports
  • SummarizedExperiment * imports
  • bambu * imports
  • basilisk * imports
  • circlize * imports
  • cowplot * imports
  • dplyr * imports
  • ggbio * imports
  • ggplot2 * imports
  • grid * imports
  • gridExtra * imports
  • igraph * imports
  • magrittr * imports
  • reticulate * imports
  • rtracklayer * imports
  • scater * imports
  • scran * imports
  • scuttle * imports
  • stats * imports
  • stringr * imports
  • tidyr * imports
  • utils * imports
  • withr * imports
  • zlibbioc * imports
  • BiocFileCache * suggests
  • BiocStyle * suggests
  • knitr * suggests
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  • rmarkdown * suggests
.github/workflows/check-bioc.yml actions
  • actions/cache v2 composite
  • actions/checkout v2 composite
  • actions/upload-artifact master composite
  • docker/build-push-action v1 composite
  • r-lib/actions/setup-pandoc v2 composite
  • r-lib/actions/setup-r v2 composite