| MAQMapQA-class |
(Legacy) Quality assessment summaries from MAQ map files |
| QualityScore |
Construct objects indicating read or alignment quality |
| SRUtil-class |
".SRUtil" and related classes |
| SRSet-class |
(Legacy) A base class for Roche experiment-wide data |
| ShortReadQA-class |
Quality assessment of fastq files and ShortReadQ objects |
| ExperimentPath-class |
(Legacy) "ExperimentPath" class representing a file hierarchy of data
files |
| Intensity-class |
(Legacy) "Intensity", "IntensityInfo", and "IntensityMeasure" base
classes for short read image intensities |
| alphabetByCycle |
Summarize nucleotide, amino acid, or quality scores by cycle |
| ShortRead-deprecated |
Deprecated functions from the ShortRead package |
| SRFilterResult-class |
"SRFilterResult" for SRFilter output and statistics |
| .QA-class |
Virtual class for representing quality assessment results |
| SolexaIntensity-class |
Classes "SolexaIntensity" and "SolexaIntensityInfo" |
| QualityScore-class |
Quality scores for short reads and their alignments |
| ShortRead-class |
"ShortRead" class for short reads |
| readAligned |
(Legacy) Read aligned reads and their quality scores into R representations |
| renewable |
Renew (update) a ShortRead object with new values |
| Snapshot-class |
Class "Snapshot" |
| accessors |
(Legacy) Accessors for ShortRead classes |
| SolexaSet-class |
(Legacy) "SolexaSet" coordinating Solexa output locations with sample annotations |
| readQseq |
(Legacy) Read Solexa qseq files as fastq-style quality scores |
| ShortReadQ-class |
"ShortReadQ" class for short reads and their quality scores |
| ShortReadBase-package |
FASTQ input and manipulation.
|
| readBaseQuality |
(Legacy) Read short reads and their quality scores into R representations |
| clean |
Remove sequences with ambiguous nucleotides from short read classes |
| tables |
Summarize XStringSet read frequencies |
| readPrb |
(Legacy) Read Solexa prb files as fastq-style quality scores |
| readBfaToc |
(Legacy) Get a list of the sequences in a Maq .bfa file |
| AlignedRead-class |
(Legacy) "AlignedRead" class for aligned short reads |
| RtaIntensity |
(Legacy) Construct objects of class "RtaIntensity" |
| qa |
Perform quality assessment on short reads |
| alphabetScore |
Efficiently calculate the sum of quality scores across bases |
| deprecated |
Deprecated and defunct functions |
| report |
Summarize quality assessment results into a report |
| srFilter |
Functions for user-created and built-in ShortRead filters |
| BowtieQA-class |
(Legacy) Quality assessment summaries from Bowtie files |
| RtaIntensity-class |
(Legacy) Class "RtaIntensity" |
| AlignedDataFrame-class |
(Legacy) "AlignedDataFrame" representing alignment annotations as a data frame
|
| QA-class |
(Updated) classes for representing quality assessment results |
| RocheSet-class |
(Legacy) Roche (454) experiment-wide data container |
| SolexaExportQA-class |
(Legacy) Quality assessment summaries from Solexa export and
realign files |
| dustyScore |
Summarize low-complexity sequences |
| SnapshotFunction-class |
Class "SnapshotFunction" |
| readFastq |
Read and write FASTQ-formatted files |
| srdistance |
Edit distances between reads and a small number of short references |
| trimTails |
Trim ends of reads based on nucleotides or qualities |
| readFasta |
Read and write FASTA files to or from ShortRead objects |
| AlignedDataFrame |
(Legacy) AlignedDataFrame constructor |
| AlignedRead |
(Legacy) Construct objects of class "AlignedRead" |
| SpTrellis-class |
Class "SpTrellis" |
| spViewPerFeature |
Tools to visualize genomic data
|
| qa2 |
(Updated) quality assessment reports on short reads |
| readXStringColumns |
Read one or more columns into XStringSet (e.g., DNAStringSet) objects
|
| countLines |
Count lines in all (text) files in a directory whose file name
matches a pattern |
| filterFastq |
Filter fastq from one file to another |
| Utilites |
Utilities for common, simple operations |
| srduplicated |
Order, sort, and find duplicates in XStringSet objects |
| SRFilter-class |
"SRFilter" for representing functions operating on ShortRead objects |
| SolexaIntensity |
(Legacy) Construct objects of class "SolexaIntensity" and
"SolexaIntensityInfo" |
| SolexaPath-class |
(Legacy) "SolexaPath" class representing a standard output file hierarchy |
| FastqFile-class |
Sampling and streaming records from fastq files |
| readIntensities |
(Legacy) Read Illumina image intensity files |
| RochePath-class |
(Legacy) "RochePath" class representing a Roche (454) experiment location |
| No Results! |