infercnv - infercnv release v1.3.3

Significant speed up of plot_cnv(), more significant the bigger the matrix. Now also reuses stored hclust for references.

- R
Published by GeorgescuC over 6 years ago

infercnv - InferCNV Release v0.99.7

Numerous fixes have been made. Improved when subclustering is done to be more accurate.

- R
Published by GeorgescuC over 7 years ago

infercnv - InferCNV Release v0.99.0

This is a large update to inferCVN, including: -more flexible infercnv::run() method -resume-level functionality, so it will reuse existing processed data objects on re-running with different parameters. -additional denoising methods included -CNV predictions using hidden Markov models.

The wiki documentation has been heavily revised to reflect the updated functionality and usage.

- R
Published by GeorgescuC over 7 years ago

infercnv - InferCNV Release v0.8.2

uses zero-inflated negative binomial to simulate spike-ins used for scaling.

- R
Published by brianjohnhaas over 7 years ago

infercnv - InferCNV Release v0.8.1

patch release - fixes a bug that impacted the multi-patient view where some cells were switching between patient panels, dependent on a mixed ordering within the cell annotations file.

- R
Published by brianjohnhaas over 7 years ago

infercnv - InferCNV Release v0.8.0

This is a major update to InferCNV. See updated wiki documentation for new usage info.

- R
Published by brianjohnhaas over 7 years ago

infercnv - InferCNV Release v0.3

``` -includes additional options:

   --ref_subtract_method=REFERENCE_SUBTRACTION_METHOD
    Method used to subtract the reference values from the observations. Valid choices are:  by_mean, by_quantiles  [Default by_mean]

    --hclust_method=HIERARCHICAL_CLUSTERING_METHOD
    Method used for hierarchical clustering of cells. Valid choices are:  ward.D, ward.D2, single, complete, average, mcquitty, median, centroid  [Default complete]

The --steps parameter now generates a full inferCNV heatmap/plot for each of the data transformation operations performed.

The log transformation log2(x/10 + 1) to generate transcripts(or counts) per 100k instead of per million is now more simply log2(x+1). If the user wants to study counts-per-100k or counts-per-10k, that is entirely fine... The log transformation will simply be log2(whatever + 1).

-sample data is updated using a random selection of 400 malignant oligodendroglioma cells and ~100 normal cells, described in file '_sampledcells.annotations.dat'. The actual gene names and cell names are provided instead of the generic gene_ and cell_ values. Data is from Tirosh et al. Nature 2016. ```

- R
Published by brianjohnhaas about 8 years ago

infercnv - infercnv-v0.2

Now, works with R version >= 3.2

- R
Published by vrushali-broad over 8 years ago

infercnv - InferCNV as a library or script.

InferCNV can now be installed as a library from the associated tar.gz or directly from GitHub.

If installing from the tar.gz, use the following command on command line. R CMD install infercnv_0.1.tar.gz

If installing from GitHub, use the following command in R. library("devtools") install_github("broadinstitute/inferCNV")

- R
Published by TimothyTickle about 9 years ago