/usr/lib/R/site-library/ShortRead/INDEX is in r-bioc-shortread 1.36.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 | .QA-class Virtual class for representing quality
assessment results
.SRUtil-class ".SRUtil" and related classes
AlignedDataFrame (Legacy) AlignedDataFrame constructor
AlignedDataFrame-class
(Legacy) "AlignedDataFrame" representing
alignment annotations as a data frame
AlignedRead (Legacy) Construct objects of class
"AlignedRead"
AlignedRead-class (Legacy) "AlignedRead" class for aligned short
reads
BowtieQA-class (Legacy) Quality assessment summaries from
Bowtie files
ExperimentPath-class (Legacy) "ExperimentPath" class representing a
file hierarchy of data files
FastqFile-class Sampling and streaming records from fastq files
FastqQA Quality assessment of fastq files and
ShortReadQ objects
Intensity-class (Legacy) "Intensity", "IntensityInfo", and
"IntensityMeasure" base classes for short read
image intensities
MAQMapQA-class (Legacy) Quality assessment summaries from MAQ
map files
NumericQuality Construct objects indicating read or alignment
quality
QA-class (Updated) classes for representing quality
assessment results
QualityScore-class Quality scores for short reads and their
alignments
RochePath-class (Legacy) "RochePath" class representing a Roche
(454) experiment location
RocheSet-class (Legacy) Roche (454) experiment-wide data
container
RtaIntensity (Legacy) Construct objects of class
"RtaIntensity"
RtaIntensity-class (Legacy) Class "RtaIntensity"
SRFilter-class "SRFilter" for representing functions operating
on ShortRead objects
SRFilterResult-class "SRFilterResult" for SRFilter output and
statistics
SRSet-class (Legacy) A base class for Roche experiment-wide
data
ShortRead-class "ShortRead" class for short reads
ShortReadBase-package FASTQ input and manipulation.
ShortReadQ-class "ShortReadQ" class for short reads and their
quality scores
Snapshot-class Class '"Snapshot"'
SnapshotFunction-class
Class "SnapshotFunction"
SolexaExportQA-class (Legacy) Quality assessment summaries from
Solexa export and realign files
SolexaIntensity (Legacy) Construct objects of class
"SolexaIntensity" and "SolexaIntensityInfo"
SolexaIntensity-class Classes "SolexaIntensity" and
"SolexaIntensityInfo"
SolexaPath-class (Legacy) "SolexaPath" class representing a
standard output file hierarchy
SolexaSet-class (Legacy) "SolexaSet" coordinating Solexa output
locations with sample annotations
SpTrellis-class Class "SpTrellis"
accessors (Legacy) Accessors for ShortRead classes
alphabetByCycle Summarize nucleotide, amino acid, or quality
scores by cycle
alphabetScore Efficiently calculate the sum of quality scores
across bases
clean Remove sequences with ambiguous nucleotides
from short read classes
countLines Count lines in all (text) files in a directory
whose file name matches a pattern
deprecated Deprecated and defunct functions
dustyScore Summarize low-complexity sequences
filterFastq Filter fastq from one file to another
polyn Utilities for common, simple operations
qa Perform quality assessment on short reads
qa2 (Updated) quality assessment reports on short
reads
readAligned (Legacy) Read aligned reads and their quality
scores into R representations
readBaseQuality (Legacy) Read short reads and their quality
scores into R representations
readBfaToc (Legacy) Get a list of the sequences in a Maq
.bfa file
readFasta Read and write FASTA files to or from ShortRead
objects
readFastq Read and write FASTQ-formatted files
readIntensities (Legacy) Read Illumina image intensity files
readPrb (Legacy) Read Solexa prb files as fastq-style
quality scores
readQseq (Legacy) Read Solexa qseq files as fastq-style
quality scores
readXStringColumns Read one or more columns into XStringSet (e.g.,
DNAStringSet) objects
renewable Renew (update) a ShortRead object with new
values
report Summarize quality assessment results into a
report
spViewPerFeature Tools to visualize genomic data
srFilter Functions for user-created and built-in
ShortRead filters
srdistance Edit distances between reads and a small number
of short references
srduplicated Order, sort, and find duplicates in XStringSet
objects
tables Summarize XStringSet read frequencies
trimTails Trim ends of reads based on nucleotides or
qualities
uniqueFilter Deprecated functions from the ShortRead package
|