Release Notes¶
v 1.0.0¶
- First public release.
v 1.1.7¶
bulk module:¶
- Added Deseq2, including
pyDEseq
functions:deseq2_normalize
,estimateSizeFactors
,estimateDispersions
,Matrix_ID_mapping
. - Included TCGA with
TCGA
. - Introduced Enrichment with functions
geneset_enrichment
,geneset_plot
.
single module:¶
- Integrated scdrug with functions
autoResolution
,writeGEP
,Drug_Response
. - Added cpdb with functions
cpdb_network_cal
,cpdb_plot_network
,cpdb_plot_interaction
,cpdb_interaction_filtered
. - Included scgsea with functions
geneset_aucell
,pathway_aucell
,pathway_aucell_enrichment
,pathway_enrichment
,pathway_enrichment_plot
.
v 1.1.8¶
single module:¶
- Addressed errors in cpdb, including import errors and color issues in
cpdb_plot_network
. - Introduced
cpdb_submeans_exacted
in cpdb for easy sub-network extraction.
v 1.1.9¶
bulk2single module:¶
- Added the
bulk2single
module. - Fixed model load error from bulk2space.
- Resolved early stop issues from bulk2space.
- Included more user-friendly input methods and visualizations.
- Added loss history visualization.
utils module:¶
- Introduced
pyomic_palette
in the plot module.
v 1.1.10¶
- Updated all code references.
single module:¶
- Fixed non-valid parameters in
single.mofa.mofa_run
function. - Added layer raw count addition in
single.scanpy_lazy
function. - Introduced
utils.plot_boxplot
for plotting box plots with jittered points. - Added
bulk.pyDEseq.plot_boxplot
for plotting box plots with jittered points for specific genes.
v 1.2.0¶
bulk module:¶
- Fixed non-valid
cutoff
parameter inbulk.geneset_enrichment
. - Added modules:
pyPPI
,pyGSEA
,pyWGCNA
,pyTCGA
,pyDEG
.
bulk2single module:¶
- Introduced
bulk2single.save
for manual model saving.
v 1.2.1-4¶
single module:¶
- Added
pySCSA
module with functions:cell_anno
,cell_anno_print
,cell_auto_anno
,get_model_tissue
. - Implemented doublet cell filtering in
single.scanpy_lazy
. - Added
single.scanpy_cellanno_from_dict
for easier annotation. - Updated SCSA database from CellMarker2.0.
- Fixed errors in SCSA database keys:
Ensembl_HGNC
andEnsembl_Mouse
.
v 1.2.5¶
single module:¶
- Added
pyVIA
module with functions:run
,plot_piechart_graph
,plot_stream
,plot_trajectory_gams
,plot_lineage_probability
,plot_gene_trend
,plot_gene_trend_heatmap
,plot_clustergraph
. - Fixed warning error in
utils.pyomic_plot_set
. - Updated requirements, including
pybind11
,hnswlib
,termcolor
,pygam
,pillow
,gdown
.
v 1.2.6¶
single module:¶
- Added
pyVIA.get_piechart_dict
andpyVIA.get_pseudotime
.
v 1.2.7¶
bulk2single module:¶
- Added
Single2Spatial
module with functions:load
,save
,train
,spot_assess
. - Fixed installation errors for packages in pip.
v 1.2.8¶
- Fixed pip installation errors.
bulk2single module:¶
- Replaced
deep-forest
inSingle2Spatial
withNeuron Network
for classification tasks. - Accelerated the entire Single2Spatial inference process using GPU and batch-level estimation by modifying the
predicted_size
setting.
v 1.2.9¶
bulk module:¶
- Fixed duplicates_index mapping in
Matrix_ID_mapping
. - Resolved hub genes plot issues in
pyWGCNA.plot_sub_network
. - Fixed backupgene in
pyGSEA.geneset_enrichment
to support rare species. - Added matrix plot module in
pyWGCNA.plot_matrix
.
single module:¶
- Added
rank_genes_groups
check inpySCSA
.
bulk2single module:¶
- Fixed import error of
deepforest
.
v 1.2.10¶
- Renamed the package to
omicverse
.
single module:¶
- Fixed argument error in
pySCSA
.
bulk2single module:¶
- Updated plot arguments in
bulk2single
.
v 1.2.11¶
bulk module:¶
- Fixed
wilcoxon
method inpyDEG.deg_analysis
. - Added parameter setting for treatment and control group names in
pyDEG.plot_boxplot
. - Fixed figure display issues in
pyWGCNA.plot_matrix
. - Fixed category correlation failed by one-hot in
pyWGCNA.analysis_meta_correlation
. - Fixed network display issues in
pyWGCNA.plot_sub_network
and updatedutils.plot_network
to avoid errors.
v 1.3.0¶
bulk module:¶
- Added
DEseq2
method topyDEG.deg_analysis
. - Introduced
pyGSEA
module inbulk
. - Renamed raw
pyGSEA
topyGSE
inbulk
. - Added
get_gene_annotation
inutils
for gene name transformation.
v 1.3.1¶
single module:¶
- Added
get_celltype_marker
method.
single module:¶
- Added
GLUE_pair
,pyMOFA
,pyMOFAART
module. - Added tutorials for
Multi omics analysis by MOFA and GLUE
. - Updated tutorial for
Multi omics analysis by MOFA
.
v 1.4.0¶
bulk2single module:¶
- Added
BulkTrajBlend
method.
single module:¶
- Fixed errors in
scnocd
model. - Added
save
,load
, andget_pair_dict
inscnocd
model.
utils module:¶
- Added
mde
method. - Added
gz
format support forutils.read
.
v 1.4.1¶
preprocess module:¶
- Added
pp
(preprocess) module withqc
(quantity control),hvg
(high variable feature),pca
. - Added
data_files
for cell cycle calculation from Cellula and pegasus.
v 1.4.3¶
¶
preprocess module:
- Fixed sparse preprocess error in pp
.
- Fixed trajectory import error in via
.
- Added gene correlation analysis of trajectory.
v 1.4.4¶
single module:¶
- Added
panglaodb
database topySCSA
module. - Fixed errors in
pySCSA.cell_auto_anno
when some cell types are not found in clusters. - Fixed errors in
pySCSA.cell_anno
whenrank_genes_groups
are not consistent with clusters. - Added
pySIMBA
module in single for batch correction.
preprocess module:¶
- Added
store_layers
andretrieve_layers
inov.utils
. - Added
plot_embedding_celltype
andplot_cellproportion
inov.utils
.
v 1.4.5¶
single module:¶
- Added
MetaTiME
module to perform cell type annotation automatically in TME.
v 1.4.12¶
- Updated
conda install omicverse -c conda-forge
.
single module:¶
- Added
pyTOSICA
module to perform cell type migration from reference scRNA-seq in Transformer model. - Added
atac_concat_get_index
,atac_concat_inner
,atac_concat_outer
functions to merge/concatenate scATAC data. - Fixed
MetaTime.predicted
when Unknown cell type appears.
preprocess module:¶
- Added
plot_embedding
inov.utils
to plot UMAP in a special color dictionary.
v 1.4.13¶
bulk module:¶
- Added
mad_filtered
to filter robust genes when calculating the network inov.bulk.pyWGCNA
module. - Fixed
string_interaction
inov.bulk.pyPPI
for string-db updates.
preprocess module:¶
- Changed
mode
argument ofpp.preprocess
to control preprocessing steps. - Added
ov.utils.embedding
,ov.utils.neighbors
, andov.utils.stacking_vol
.
v 1.4.14¶
preprocess module:¶
- Added
batch_key
inpp.preprocess
andpp.qc
.
utils module:¶
- Added
plot_ConvexHull
to visualize the boundary of clusters. - Added
weighted_knn_trainer
andweighted_knn_transfer
for multi-adata integration.
single module:¶
- Fixed import errors in
mofa
.
v 1.4.17¶
bulk module:¶
- Fixed compatibility issues with
pydeseq2
version0.4.0
. - Added
bulk.batch_correction
for multi-bulk RNA-seq/microarray samples.
single module:¶
- Added
single.batch_correction
for multi-single cell datasets.
preprocess module:¶
- Added parameter
layers_add
inpp.scale
.
v 1.5.0¶
single module:¶
- Added
cellfategenie
to calculate timing-associated genes/genesets. - Fixed the name error in
atac_concat_outer
. - Added more kwargs for
batch_correction
.
utils module:¶
- Added
plot_heatmap
to visualize the heatmap of pseudotime. - Fixed
embedding
when the version ofmpl
is larger than3.7.0
. - Added
geneset_wordcloud
to visualize geneset heatmaps of pseudotime.
v 1.5.1¶
single module:¶
- Added
scLTNN
to infer cell trajectory.
bulk2single module:¶
- Updated cell fraction prediction with
TAPE
in bulk2single. - Fixed group and normalization issues in bulk2single.
utils module:¶
- Added
Ro/e
calculation (by: Haihao Zhang). - Added
cal_paga
andplot_paga
to visualize the state transfer matrix. - Fixed the
read
function.
v 1.5.2¶
bulk2single Module:¶
- Resolved a matrix error occurring when gene symbols are not unique.
- Addressed the
interpolation
issue inBulkTrajBlend
when target cells do not exist. - Corrected the
generate
function inBulkTrajBlend
. - Rectified the argument for
vae_configure
inBulkTrajBlend
whencell_target_num
is set to None. - Introduced the parameter
max_single_cells
for input inBulkTrajBlend
. - Defaulted to using
scaden
for deconvolution in Bulk RNA-seq.
single Module:¶
- Fixed an error in
pyVIA
when the root is set to None. - Added the
TrajInfer
module for inferring cell trajectories. - Integrated
Palantir
andDiffusion_map
into theTrajInfer
module. - Corrected the parameter error in
batch_correction
.
utils Module:¶
- Introduced
plot_pca_variance_ratio
for visualizing the ratio of PCA variance. - Added the
cluster
andfiltered
module for clustering the cells - Integrated
MiRA
to calculate the LDA topic
v 1.5.3¶
single Module:¶
- Added
scVI
andMIRA
to remove batch effect
space Module:¶
- Added
STAGATE
to cluster and denoisy the spatial RNA-seq
pp Module:¶
- Added
doublets
argument ofov.pp.qc
to control doublets('Default'=True)
v 1.5.4¶
bulk Module:¶
- Fixed an error in
pyDEG.deg_analysis
whenn_cpus
can not be set inpyDeseq2(v0.4.3)
single Module:¶
- Fixed an argument error in
single.batch_correction
of combat
utils Module:¶
- Added
venn4
plot to visualize - Fixed the label visualization of
plot_network
- Added
ondisk
argument ofLDA_topic
space Module:¶
- Added
Tangram
to mapping the scRNA-seq to stRNA-seq
v 1.5.5¶
pp Module:¶
- Added
max_cells_ratio
andmax_genes_ratio
to control the max threshold in qc of scRNA-seq
single Module:¶
- Added
SEACells
model to calculate the metacells from scRNA-seq
space Module:¶
- Added
STAligner
to integrate multi stRNA-seq
v 1.5.6¶
pp Module¶
- Added
mt_startswith
argument to control theqc
in mouse or other species.
utils Module¶
- Added
schist
method to cluster the single cell RNA-seq
single Module¶
- Fixed the import error of
palantir
in SEACells - Added
CEFCON
model to identify the driver regulators of cell fate decisions
bulk2single Module¶
- Added
use_rep
andneighbor_rep
argument to configure the nocd
space Module¶
- Added
SpaceFlow
to identify the pseudo-spatial map
v 1.5.8¶
pp Module¶
- Added
score_genes_cell_cycle
function to calculate the cell cycle
bulk Module¶
- Fixed
dds.plot_volcano
text plot error when the version ofadjustText
larger than0.9
single Module¶
- Optimised
MetaCell.load
model loading logic - Fixed an error when loading the model usng
MetaCell.load
- Added tutorials of
Metacells
pl Module¶
Add pl
as a unified drawing prefix for the next release, to replace the drawing functionality in the original utils, while retaining the drawing in the original utils.
- Added
embedding
to plot the embedding of scRNA-seq usingov.pl.embedding
- Added
optim_palette
to provide a spatially constrained approach that generates discriminate color assignments for visualizing single-cell spatial data in various scenarios - Added
cellproportion
to plot the proportion of stack bar of scRNA-seq - Added
embedding_celltype
to plot the figures both celltype proportion and embedding - Added
ConvexHull
to plot the ConvexHull around the target cells - Added
embedding_adjust
to adjust the text of celltype legend in embedding - Added
embedding_density
to plot the category density in the cells - Added
bardotplot
to plot the bardotplot between different groups. - Added
add_palue
to plot the p-threshold between different groups. - Added
embedding_multi
to support themudata
object - Added
purple_color
to visualize the purple palette. - Added
venn
to plot the venn from set 2 to set 4 - Added
boxplot
to visualize the boxdotplot - Added
volcano
to visualzize the result of differential expressed genes
v 1.5.9¶
single Module¶
- Added
slingshot
insingle.TrajInfer
- Fixed some error of
scLTNN
- Added
GPU
mode to preprocess the data - Added
cNMF
to calculate the nmf
space Module¶
- Added
Spatrio
to mapping the scRNA-seq to stRNA-seq