Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / Bioconductor/HDF5Array issues and pull requests

#62 - Error in saveHDF5SummarizedExperiment

Issue - State: closed - Opened by fernandafranca 10 months ago - 2 comments

#61 - `H5SparseMatrix` coercion to `dgCmatrix` discards NAs

Issue - State: closed - Opened by LTLA about 1 year ago - 1 comment

#60 - installation of package ‘HDF5Array’ had non-zero exit status

Issue - State: closed - Opened by mick42-star about 1 year ago - 14 comments

#59 - Add support for seurat hdf5 format.

Pull Request - State: open - Opened by yduanBioinfo about 1 year ago - 1 comment

#58 - Release 3 16

Pull Request - State: closed - Opened by yduanBioinfo over 1 year ago - 2 comments

#57 - Add support for h5seurat object.

Pull Request - State: closed - Opened by yduanBioinfo over 1 year ago - 2 comments

#56 - Interpreting `NATIVE_UINT8` as integer in sparse matrices

Issue - State: open - Opened by LTLA over 1 year ago - 3 comments

#55 - Error with `read_block()` when using `writeHDF5Array()`

Issue - State: closed - Opened by frederikziebell over 1 year ago - 4 comments

#54 - Expose dimension and format options for the H5SparseMatrixSeed constructor

Issue - State: closed - Opened by LTLA over 1 year ago - 3 comments

#53 - Problem installing HDF5Array on R 4.3.0

Issue - State: closed - Opened by AndreaRP over 1 year ago - 2 comments

#52 - HDF5Array installation issue

Issue - State: closed - Opened by ytakemon about 2 years ago - 3 comments

#51 - Object '.replace_dir' not found

Issue - State: closed - Opened by BBBBunnyZ about 2 years ago - 2 comments

#50 - Feature Request: Support for writing sparse matrices to H5AD files

Issue - State: open - Opened by mojaveazure over 2 years ago - 7 comments
Labels: enhancement

#49 - use TENxMatrix hasn't feature name

Issue - State: closed - Opened by Liripo over 2 years ago - 3 comments

#48 - Coerce non-integer shapes into integers in the `H5SparseMatrix` constructor

Issue - State: closed - Opened by LTLA over 2 years ago - 2 comments

#47 - Cannot read 10X h5

Issue - State: closed - Opened by ekernf01 about 3 years ago - 3 comments

#46 - `superclass "DataTable_OR_NULL" not defined` error

Issue - State: closed - Opened by ekernf01 about 3 years ago - 3 comments

#45 - Direct converters from H5SparseMatrixSeed-containing DelayedMatrix to dgCMatrix

Issue - State: closed - Opened by LTLA over 3 years ago - 3 comments

#44 - Loss of sparsity when diving by vector

Issue - State: closed - Opened by const-ae over 3 years ago - 2 comments

#42 - Generalizing the H5SparseMatrixSeed class to support other data locations

Issue - State: closed - Opened by LTLA over 3 years ago - 4 comments

#41 - How to create a huge on-disk array directly from R

Issue - State: closed - Opened by kokitsuyuzaki over 3 years ago - 4 comments

#40 - H5ADMatrix objects looking up the wrong names

Issue - State: closed - Opened by LTLA over 3 years ago - 7 comments

#39 - export utility functions and add documentation page

Pull Request - State: closed - Opened by LiNk-NY over 3 years ago - 3 comments

#38 - exporting useful internal helper functions

Issue - State: closed - Opened by LiNk-NY over 3 years ago - 1 comment

#37 - H5ADMatrix block processing fails because of the dimnames

Issue - State: closed - Opened by LTLA over 3 years ago - 1 comment

#36 - Dual matrix seeds for efficient row/column accesses

Issue - State: closed - Opened by LTLA almost 4 years ago - 7 comments

#35 - Can't install HDF5Array_1.19.3 in R 4.1.0

Issue - State: closed - Opened by dpelegri almost 4 years ago - 4 comments

#34 - Extending TENxMatrix to work on variants of HDF5-backed storage

Issue - State: closed - Opened by LTLA almost 4 years ago - 16 comments

#33 - Treating dense HDF5Matrices as sparse for greater efficiency

Issue - State: closed - Opened by LTLA about 4 years ago - 8 comments

#32 - filepath in HDF5ArraySeed's validity method be extracted with path()?

Issue - State: open - Opened by LTLA about 4 years ago - 1 comment

#31 - reset_h5_location operation?

Issue - State: closed - Opened by vjcitn over 4 years ago - 12 comments

#30 - write_block fails for SparseArraySeed

Issue - State: closed - Opened by LTLA over 4 years ago - 1 comment

#29 - [Windows-only] Error realizing matrix with dimnames to HDF5Matrix

Issue - State: closed - Opened by PeteHaitch over 4 years ago - 5 comments

#27 - Coercion of large HDF5Matrix to SparseArraySeed fails

Issue - State: closed - Opened by LTLA over 4 years ago - 7 comments

#26 - taking a single row from a TENxMatrix object is extremely slow

Issue - State: closed - Opened by ccshao over 4 years ago - 4 comments

#25 - 'type' related error persists with 1yo HDF5SummarizedExperiment

Issue - State: closed - Opened by vjcitn over 4 years ago - 1 comment

#24 - Long colnames get truncated

Issue - State: closed - Opened by FelixTheStudent almost 5 years ago - 3 comments

#23 - Storing raw-Rle with RleArray on a HDF5Array backend

Issue - State: closed - Opened by rcastelo almost 5 years ago - 7 comments

#22 - Added the maxdim argument

Pull Request - State: closed - Opened by muschellij2 almost 5 years ago - 1 comment

#21 - Install eror

Issue - State: closed - Opened by kvshams about 5 years ago - 4 comments

#19 - Migrating code to allow beachmat to read HDF5Matrix objects

Pull Request - State: closed - Opened by LTLA about 5 years ago - 1 comment

#18 - HDF5Matrix subsetting loads subset into memory

Issue - State: closed - Opened by avalcarcel9 over 5 years ago - 4 comments

#17 - Support for contiguous layout HDF5

Issue - State: closed - Opened by soulj over 5 years ago - 3 comments

#16 - Reshape array to Matrix without reading in

Issue - State: closed - Opened by muschellij2 over 5 years ago - 1 comment

#15 - Migrating beachmat's HDF5-related code to HDF5Array

Issue - State: closed - Opened by LTLA almost 6 years ago - 11 comments

#14 - Is it possible to connect to a HDF5 file in a read-only manner?

Issue - State: closed - Opened by phaverty almost 6 years ago - 2 comments

#13 - Can HDF5Array persist the dimnames too?

Issue - State: closed - Opened by phaverty almost 6 years ago - 3 comments

#12 - Can HDF5Matrix and RLEMatrix work together?

Issue - State: closed - Opened by phaverty almost 6 years ago - 9 comments

#11 - Open up API for loadHDF5SummarizedExperiment

Issue - State: closed - Opened by LiNk-NY almost 6 years ago - 6 comments

#10 - Ideas for improvement to saveHDF5SummarizedExperiment()

Issue - State: closed - Opened by PeteHaitch over 6 years ago - 5 comments

#9 - Possible to delay updateObject() in loadHDF5SummarizedExperiment()?

Issue - State: closed - Opened by PeteHaitch over 6 years ago - 6 comments

#8 - Use DelayedArray:::set_dimnames()

Pull Request - State: closed - Opened by PeteHaitch over 6 years ago - 1 comment

#7 - Use DelayedArray:::set_dimnames()

Pull Request - State: closed - Opened by PeteHaitch over 6 years ago - 5 comments

#6 - HDF5Array show method recurses infinitely

Issue - State: closed - Opened by LTLA over 6 years ago - 2 comments

#5 - 1.7.6 build error

Issue - State: closed - Opened by pati-ni almost 7 years ago - 2 comments

#4 - 1.7

Issue - State: closed - Opened by pati-ni almost 7 years ago

#3 - Fix typo in writeHDF5Array.Rd

Pull Request - State: closed - Opened by PeteHaitch almost 7 years ago - 1 comment

#2 - Can we avoid 'degrading' a HDF5Array to a DelayedArray upon subsetting?

Issue - State: closed - Opened by PeteHaitch about 7 years ago - 2 comments

#1 - 1.5-2x speed-up for as.matrix(HDF5Matrix)

Issue - State: closed - Opened by PeteHaitch about 7 years ago - 6 comments