epiG: DNA methylation and SNP calling for bisulfite sequencing data

DNA methylation and SNP calling for bisulfite sequencing data.

AuthorMartin Vincent
Date of publication2015-05-22 10:05:07
MaintainerMartin Vincent <vincent@math.ku.dk>
LicenseGPL (>= 2)
Version1.0.0

View on R-Forge

Functions

chain.info Man page
chain.info.epiG Man page
compute_chunk_positions Man page
coverage Man page
coverage.epiG Man page
create_bisulfite_model Man page
create_error_distributions Man page
create_genotype_prior_alt Man page
create_genotype_prior_ref Man page
end Man page
end.epiG Man page
epiG Man page
epiG.algorithm.config Man page
epiG.chunks Man page
exp_decay Man page
fetch_alt Man page
fetch.reads Man page
fetch_reads_info Man page
fetch_ref Man page
genotype Man page
genotype.epiG Man page
length.epiG Man page
locate.DGCH Man page
locate.GCH Man page
locate.HCGD Man page
locate.SNP Man page
methylation Man page
methylation.epiG Man page
nchain Man page
nchain.epiG Man page
nchunks Man page
nchunks.epiG Man page
nread Man page
nread.epiG Man page
position.info Man page
position.info.epiG Man page
print.epiG Man page
print.epiG.config Man page
read.fasta Man page
read.info Man page
read.info.epiG Man page
start Man page
start.epiG Man page
strand Man page
strand.epiG Man page
subregion Man page
subregion.epiG Man page
symbols Man page
vector.search Man page

Files

epiG/DESCRIPTION
epiG/NAMESPACE
epiG/R
epiG/R/epiG_config.R epiG/R/epiG_fetch.R epiG/R/epiG_haplo_fit.R epiG/R/epiG_locate.R epiG/R/epiG_navigate.R epiG/R/epiG_summary.R
epiG/man
epiG/man/chain.info.Rd epiG/man/chain.info.epiG.Rd epiG/man/compute_chunk_positions.Rd epiG/man/coverage.Rd epiG/man/coverage.epiG.Rd epiG/man/create_bisulfite_model.Rd epiG/man/create_error_distributions.Rd epiG/man/create_genotype_prior_alt.Rd epiG/man/create_genotype_prior_ref.Rd epiG/man/end.Rd epiG/man/end.epiG.Rd epiG/man/epiG.Rd epiG/man/epiG.algorithm.config.Rd epiG/man/epiG.chunks.Rd epiG/man/exp_decay.Rd epiG/man/fetch.reads.Rd epiG/man/fetch_alt.Rd epiG/man/fetch_reads_info.Rd epiG/man/fetch_ref.Rd epiG/man/genotype.Rd epiG/man/genotype.epiG.Rd epiG/man/length.epiG.Rd epiG/man/locate.DGCH.Rd epiG/man/locate.GCH.Rd epiG/man/locate.HCGD.Rd epiG/man/locate.SNP.Rd epiG/man/methylation.Rd epiG/man/methylation.epiG.Rd epiG/man/nchain.Rd epiG/man/nchain.epiG.Rd epiG/man/nchunks.Rd epiG/man/nchunks.epiG.Rd epiG/man/nread.Rd epiG/man/nread.epiG.Rd epiG/man/position.info.Rd epiG/man/position.info.epiG.Rd epiG/man/print.epiG.Rd epiG/man/print.epiG.config.Rd epiG/man/read.fasta.Rd epiG/man/read.info.Rd epiG/man/read.info.epiG.Rd epiG/man/start.Rd epiG/man/start.epiG.Rd epiG/man/strand.Rd epiG/man/strand.epiG.Rd epiG/man/subregion.Rd epiG/man/subregion.epiG.Rd epiG/man/symbols.Rd epiG/man/vector.search.Rd
epiG/src
epiG/src/Makevars
epiG/src/alignment_data.h
epiG/src/arma_additions.h
epiG/src/bam_reader.h
epiG/src/chain_opt.h
epiG/src/chunked_chain_opt.h
epiG/src/epiG.cpp
epiG/src/epiG_algorithm_config.h
epiG/src/genotype_opt.h
epiG/src/math_tools.h
epiG/src/prior.h
epiG/src/rinterface
epiG/src/rinterface/epiG.h
epiG/src/rinterface/fetch.h
epiG/src/rtools
epiG/src/rtools.h
epiG/src/rtools/get_value.h
epiG/src/rtools/omp_rwarnings.h
epiG/src/rtools/rList.h
epiG/src/rtools/rObject_decl.h
epiG/src/rtools/rObject_def.h
epiG/src/samtools
epiG/src/samtools/LICENSE
epiG/src/samtools/bam.c
epiG/src/samtools/bam.h
epiG/src/samtools/bam_aux.c
epiG/src/samtools/bam_endian.h
epiG/src/samtools/bam_import.c
epiG/src/samtools/bam_index.c
epiG/src/samtools/bam_sort.c
epiG/src/samtools/bgzf.c
epiG/src/samtools/bgzf.h
epiG/src/samtools/faidx.c
epiG/src/samtools/faidx.h
epiG/src/samtools/khash.h
epiG/src/samtools/kseq.h
epiG/src/samtools/ksort.h
epiG/src/samtools/kstring.c
epiG/src/samtools/kstring.h
epiG/src/samtools/razf.c
epiG/src/samtools/razf.h
epiG/src/samtools/sam.c
epiG/src/samtools/sam.h
epiG/src/samtools/sam_header.c
epiG/src/samtools/sam_header.h
epiG/src/seq_tools.h
epiG/src/simple_timer.h
epiG/src/types.h
epiG/src/vector_search.h

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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