ngsReports - Load FastqQC reports and other NGS related files

This package provides methods and object classes for parsing FastQC reports and output summaries from other NGS tools into R. As well as parsing files, multiple plotting methods have been implemented for visualising the parsed data. Plots can be generated as static ggplot objects or interactive plotly objects.

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qualitycontrolreportwriting

8.09 score 23 stars 120 scripts 448 downloads

extraChIPs - Additional functions for working with ChIP-Seq data

This package builds on existing tools and adds some simple but extremely useful capabilities for working wth ChIP-Seq data. The focus is on detecting differential binding windows/regions. One set of functions focusses on set-operations retaining mcols for GRanges objects, whilst another group of functions are to aid visualisation of results. Coercion to tibble objects is also implemented.

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chipseqhicsequencingcoverage

6.88 score 7 stars 36 scripts 402 downloads

SimpleUpset - Create Upset Plots

Create Upset plots using a combination of 'ggplot2' and 'patchwork'.

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6.37 score 13 stars 2 dependents 3 scripts 288 downloads

motifTestR - Perform key tests for binding motifs in sequence data

Taking a set of sequence motifs as PWMs, test a set of sequences for over-representation of these motifs, as well as any positional features within the set of motifs. Enrichment analysis can be undertaken using multiple statistical approaches. The package also contains core functions to prepare data for analysis, and to visualise results.

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motifannotationchipseqchiponchipsequencematchingsoftware

4.90 score 1 stars 5 scripts 293 downloads

transmogR - Modify a set of reference sequences using a set of variants

transmogR provides the tools needed to crate a new reference genome or reference transcriptome, using a set of variants. Variants can be any combination of SNPs, Insertions and Deletions. The intended use-case is to enable creation of variant-modified reference transcriptomes for incorporation into transcriptomic pseudo-alignment workflows, such as salmon.

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alignmentgenomicvariationsequencingtranscriptomevariantvariantannotationzlib

4.78 score 6 scripts 262 downloads