NEWS.md

In hugheylab/seeker: Simplified Fetching and Processing of Microarray and RNA-Seq Data

seeker 1.1.6

• Made error handling more graceful.

seeker 1.1.5

• Added support for GPL17811 (thanks to @jacorvar).

seeker 1.1.4

• Fixed processing of ArrayExpress data (thanks to @jacorvar).
• Removed deprecated argument from biomaRt::listEnsemblArchives().

seeker 1.1.3

• Updated test for fetching metadata again.
• fetchMetadata() now orders its result.

seeker 1.1.2

• Updated test for fetching metadata.

seeker 1.1.1

• Updated test expectations for altered column order in metadata from ENA.

seeker 1.1.0

• Removed dependency on ArrayExpress package.

seeker 1.0.14

• Fixed handling of whitespace in file paths while installing miniconda.

seeker 1.0.13

• Updated for BioStudies API.

seeker 1.0.12

• fetchMetadata() can now save the metadata to a text file.

seeker 1.0.11

• Revised documentation.

seeker 1.0.10

• Revised package for CRAN.

seeker 1.0.9

• Revised "Description" text.y
• Skipped more tests on CRAN to avoid installation of packages.

seeker 1.0.8

• Removed default install directories for dependencies in installSysDeps().
• Replaced options(warn=-1) to use suppressWarnings().
• Updated description text.
• Revised console printing.

seeker 1.0.7

• Added support for more platforms.
• Added ability for seekerArray() to skip processing the expression data.

seeker 1.0.6

• Added installation of snakemake by installSysDeps() for easier reproducible analyses.

seeker 1.0.5

• Added argument to installSysDeps() to specify directory in which to create or modify .Rprofile.

seeker 1.0.4

• Skipped "getNaiveEsetAe() supported" test on CRAN due to BioConductor issues.

seeker 1.0.3

• Made getProbeGeneMapping() test check for version number of mapping package.
• Revised arguments for seekerArray() and updated tests and vignettes accordingly.

seeker 1.0.2

• Set default parent directory for seekerArray().
• Added custom CDF support for platform GPL17400.

seeker 1.0.1

• Updated seeker() to save unmodified metadata file.

seeker 1.0.0

• Updated seeker() to output info of SRA Toolkit-based dependencies.
• Revised tests and updated version number to prepare for a CRAN submission.

seeker 0.0.0.9068

• Updated run_seeker.sh to use correct conda environment.
• Updated Reproducibility vignette to not require local installation of the R package.

seeker 0.0.0.9067

• Changed species to organism for consistency with NCBI and other packages.
• Added checking for parallel backend.

seeker 0.0.0.9062

• Fixed syntax to adhere to lab code style.

hugheylab/seeker documentation built on Aug. 28, 2024, 8:20 a.m.