ALISEQ
Contents:
ALISEQ, a program for analysing RNA-Seq data
Instalation and setup
Running the allele specific expression (ASE) pipeline
Running the read simulation pipeline
Workflow
Other stuff
Python modules
ALISEQ
Docs
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Index
Index
C
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D
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E
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F
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G
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I
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M
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P
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Q
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R
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S
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T
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V
C
chooseInsert() (in module simulate_reads)
convert2bed (module)
createAltAllele() (in module simulate_reads)
createRandomSequence() (in module simulate_reads)
createRandomSequenceIndex() (in module simulate_reads)
createRandomSequenceLibrary() (in module simulate_reads)
createReadLibrary() (in module simulate_reads)
createReadPair() (in module simulate_reads)
createTestInsert() (in module simulate_reads)
csv2bed() (in module convert2bed)
D
defineCountsAndSequences() (in module simulate_reads)
E
enrichASE() (in module genewiseMAFC)
evaluate() (in module evaluate_simulation)
evaluate_simulation (module)
F
fasta() (in module simulate_reads)
fastq() (in module simulate_reads)
fastWrap() (in module simulate_reads)
G
genewiseMAFC (module)
gtf2bed() (in module convert2bed)
I
indexFasta() (in module simulate_reads)
invert() (in module simulate_reads)
M
maketable (module)
meanAbsoluteFoldChange() (in module genewiseMAFC)
mutateString() (in module simulate_reads)
P
parseHeaders() (in module simulate_reads)
prepareData() (in module simulate_reads)
processXML() (in module read_buffalo_xml_data)
Q
qualScore() (in module simulate_reads)
R
randomDecision() (in module simulate_reads)
read_buffalo_xml_data (module)
readQualscores() (in module simulate_reads)
S
simulate_reads (module)
simulateSequencingExperiment() (in module simulate_reads)
T
test_1() (in module simulate_reads)
test_2() (in module simulate_reads)
test_3() (in module simulate_reads)
test_4() (in module simulate_reads)
V
vcf2bed() (in module convert2bed)