NEWS.md

In hms-dbmi/dseqr: GUI to Explore Single-Cell and Bulk RNA-Seq from Fastq to Pathways and Perturbations

dseqr 0.22.0

• initialize import and export of R objects

dseqr 0.20.0

• switch to picker for grid plots

dseqr 0.19.0

• switch to picker for scatter plots
• add support for .h5 uploads

dseqr 0.16.0

• updated scDblFinder to 1.7.4
• improved upload modal
• support for all ensembl species
• switch to HDF5Array::TENxMatrix for fast gene exploration without loading time
• see convert script to update data generated with [v0.15.0-0.16.0) *

dseqr 0.15.0

• Added human_lung reference from azimuth
• can zoom plots with brush and double-click
• gene table has filter for each column
• see convert script to update data generated with [v0.14.1-0.15.0)

dseqr 0.14.18

• pathway analysis is faster and GO terms are clustered

dseqr 0.14.1

• can delete single-cell datasets
• improved upload interface
• added cluster-free differential expression plot
• uses dgRMatrix for faster access to logcounts
• see convert script to update data generated with v[0.14.0-0.14.1)

dseqr 0.14.0

• logcounts and SingleCellExperiment are saved separately for initial load speed
• see convert script to update data generated with v[0.13.3-0.14.0)

dseqr 0.13.3

• control and test sample can be changed through UI
• added cluster-free differential abundance plot
• see convert script to update data generated with v[0.13.1-0.13.3)

dseqr 0.13.1

• Restored 1v1 cluster comparisons now using AUC and percent differences.

dseqr 0.13.0

• Added a NEWS.md file to track changes to the package.
• Removed LoomExperiment in favor of qs::qsave(..., preset = 'fast')
• Uses presto to calculate markers for speed.
• Implements flexible integrated group specification/comparison.
• Uses scDblFinder for detecting doublets.
• Uses UMAP for larger datasets (>5000 cells).
• see convert script to update data generated with v[0.10.0-0.13.0)

hms-dbmi/dseqr documentation built on Oct. 22, 2024, 12:10 a.m.