aneuploidy.flag | Flag chromosomal aneuploidy |
bin.bam | Get read counts from BAM file |
bin.bam.2d | Get read counts between pairs of bins from BAM file |
bin.bw | Get read counts from BigWig coverage file |
breakpoint.finder.interactive | Interactive breakpoint finder |
call.abnormal.cov | Call abnormal bins |
chrplot | Chromosom plot of CNVs |
chunk.bin | Split the bins in chunks for parallel normalization |
cluster.regions | Cluster samples using their abnormal regions |
cn.plot | Plot copy-number estimates in a region. |
comp.index.files | Compress and index BED-like files |
correct.GC | Correct GC bias |
coverage.plot | Plot the bin coverage in a region |
coverage.plot.raw | Plot the raw coverage in a region |
createEmptyDF | Create empty data.frame |
draw.controls | Select control genomic regions for enrichment analysis |
fdrtool.quantile | P-values estimation |
fdrtool.quantile.2N | P-values estimation from mixture of 2 centered normal |
filter.noncovered.bins | Filter non-covered bins |
find.comparable.bins | Find comparable bins between two sample cohort. |
fragment.genome | Fragment a genome |
fragment.genome.hg19 | Fragment hg19 genome |
freq.range | Frequency computation for ranges |
gender.predict | Predict the gender of sample(s) |
getGC | GC content computation for specific bins |
getGC.hg19 | GC content computation for specific bins |
init.filenames | Init file names for analysis |
localMax | Local maximum |
mean.sd.outlierR | Mean and standard diviation after outlier removal |
med.norm | Global median normalization |
medvar.norm | Median-variance normalization of bin counts |
medvar.norm.internal | Median-variance normalization of bin counts |
mergeConsBin.cbs | Segmentation using CBS (NOT READY) |
mergeConsBin.reduce | Merge nearby bins |
mergeConsBin.simple | Simple merge of abnormal bins |
mergeConsBin.z | Merge abnormal consecutive bins |
normQC | Normalized bin count QC metrics for normalization benchmark |
norm.tm.opt | Trimmed-Mean normalization optimized |
pair.discordant.reads | Pair discordant reads |
pca.norm | PCA-based normalization of bin counts |
PopSV-package | Population-based detection of structural variants from... |
qc.sample | QC samples |
qc.samples | Join and QC the reference samples |
qc.samples.cluster | QC sample : clustering |
qc.zshift.unaffected | QC: Z-score bias in unaffected samples |
quant.norm | Quantile normalization |
quick.count | Counts reads across samples in a small number of bins |
read.bedix | Retrieve a subset of an indexed BED file. |
samples.merge | Merge data.frame across samples |
sv.summary | Abnormal regions summary |
sv.summary.interactive | Interactive summary of the calls |
tmm.norm | Trimmed-Mean M normalization |
tnK.norm | Weighted targeted normalization using K-mean optimization. |
tn.norm | Targeted-normalization of bin counts |
tn.norm.qc | QC graphs for Targeted Normalization |
tn.norm.qc.div | Targeted normalization QC: diversity of the supporting bins |
tn.test.sample | Single sample targeted normalization and test |
weight.ref.pca | Weight sample difference from a set of reference samples |
winsor | Winsorize a vector |
write.split.samples | Split and write results in one file per sample |
writeVcf | Write VCF file |
z.comp | Z-score computation |
z.norm | Z-score normalization |
z.thres.cons.bins | Z-score thresholding using bin consecutiveness. |
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