R-universe search: nanopore

Showing 5 of total 5 results (show query)

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bambu:Context-Aware Transcript Quantification from Long Read RNA-Seq data

bambu is a R package for multi-sample transcript discovery and quantification using long read RNA-Seq data. You can use bambu after read alignment to obtain expression estimates for known and novel transcripts and genes. The output from bambu can directly be used for visualisation and downstream analysis such as differential gene expression or transcript usage.

Maintained by Ying Chen. Last updated 1 months ago.

alignment coverage differentialexpression featureextraction geneexpression genomeannotation genomeassembly immunooncology longread multiplecomparison normalization rnaseq regression sequencing software transcription transcriptomics bambu bioconductor long-reads nanopore nanopore-sequencing rna-seq rna-seq-analysis transcript-quantification transcript-reconstruction cpp

18.6 match 197 stars 9.03 score 91 scripts 1 dependents

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bsseq:Analyze, manage and store whole-genome methylation data

A collection of tools for analyzing and visualizing whole-genome methylation data from sequencing. This includes whole-genome bisulfite sequencing and Oxford nanopore data.

Maintained by Kasper Daniel Hansen. Last updated 3 months ago.

dnamethylation cpp

4.0 match 37 stars 12.26 score 676 scripts 15 dependents

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NanoMethViz:Visualise methylation data from Oxford Nanopore sequencing

NanoMethViz is a toolkit for visualising methylation data from Oxford Nanopore sequencing. It can be used to explore methylation patterns from reads derived from Oxford Nanopore direct DNA sequencing with methylation called by callers including nanopolish, f5c and megalodon. The plots in this package allow the visualisation of methylation profiles aggregated over experimental groups and across classes of genomic features.

Maintained by Shian Su. Last updated 6 days ago.

software longread visualization differentialmethylation dnamethylation epigenetics dataimport zlib cpp

5.7 match 26 stars 6.95 score 11 scripts

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IONiseR:Quality Assessment Tools for Oxford Nanopore MinION data

IONiseR provides tools for the quality assessment of Oxford Nanopore MinION data. It extracts summary statistics from a set of fast5 files and can be used either before or after base calling. In addition to standard summaries of the read-types produced, it provides a number of plots for visualising metrics relative to experiment run time or spatially over the surface of a flowcell.

Maintained by Mike Smith. Last updated 5 months ago.

qualitycontrol dataimport sequencing

3.4 match 4.30 score 5 scripts

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knowYourCG:Functional analysis of DNA methylome datasets

KnowYourCG (KYCG) is a supervised learning framework designed for the functional analysis of DNA methylation data. Unlike existing tools that focus on genes or genomic intervals, KnowYourCG directly targets CpG dinucleotides, featuring automated supervised screenings of diverse biological and technical influences, including sequence motifs, transcription factor binding, histone modifications, replication timing, cell-type-specific methylation, and trait-epigenome associations. KnowYourCG addresses the challenges of data sparsity in various methylation datasets, including low-pass Nanopore sequencing, single-cell DNA methylomes, 5-hydroxymethylation profiles, spatial DNA methylation maps, and array-based datasets for epigenome-wide association studies and epigenetic clocks.

Maintained by Goldberg David. Last updated 2 months ago.

epigenetics dnamethylation sequencing singlecell spatial methylationarray zlib

0.5 match 2 stars 6.10 score 4 scripts