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bioc
ShortRead:FASTQ input and manipulation
This package implements sampling, iteration, and input of FASTQ files. The package includes functions for filtering and trimming reads, and for generating a quality assessment report. Data are represented as DNAStringSet-derived objects, and easily manipulated for a diversity of purposes. The package also contains legacy support for early single-end, ungapped alignment formats.
Maintained by Bioconductor Package Maintainer. Last updated 5 months ago.
dataimportsequencingqualitycontrolbioconductor-packagecore-packagezlibcpp
8 stars 12.08 score 1.8k scripts 49 dependents
ssnn-airr
tigger:Infers Novel Immunoglobulin Alleles from Sequencing Data
Infers the V genotype of an individual from immunoglobulin (Ig) repertoire sequencing data (AIRR-Seq, Rep-Seq). Includes detection of any novel alleles. This information is then used to correct existing V allele calls from among the sample sequences. Citations: Gadala-Maria, et al (2015) <doi:10.1073/pnas.1417683112>, Gadala-Maria, et al (2019) <doi:10.3389/fimmu.2019.00129>.
Maintained by Susanna Marquez. Last updated 3 months ago.
5.86 score 120 scripts 1 dependentsbioc
sangeranalyseR:sangeranalyseR: a suite of functions for the analysis of Sanger sequence data in R
This package builds on sangerseqR to allow users to create contigs from collections of Sanger sequencing reads. It provides a wide range of options for a number of commonly-performed actions including read trimming, detecting secondary peaks, and detecting indels using a reference sequence. All parameters can be adjusted interactively either in R or in the associated Shiny applications. There is extensive online documentation, and the package can outputs detailed HTML reports, including chromatograms.
Maintained by Kuan-Hao Chao. Last updated 27 days ago.
geneticsalignmentsequencingsangerseqpreprocessingqualitycontrolvisualizationgui
5.76 score 46 scripts
larssnip
microseq:Basic Biological Sequence Handling
Basic functions for microbial sequence data analysis. The idea is to use generic R data structures as much as possible, making R data wrangling possible also for sequence data.
Maintained by Lars Snipen. Last updated 10 months ago.
3 stars 5.46 score 54 scripts 3 dependents
protviz
prozor:Minimal Protein Set Explaining Peptide Spectrum Matches
Determine minimal protein set explaining peptide spectrum matches. Utility functions for creating fasta amino acid databases with decoys and contaminants. Peptide false discovery rate estimation for target decoy search results on psm, precursor, peptide and protein level. Computing dynamic swath window sizes based on MS1 or MS2 signal distributions.
Maintained by Witold Wolski. Last updated 5 months ago.
softwaremassspectrometryproteomicsexperimenthubsoftware
6 stars 4.45 score 93 scripts