New function log_snakemake() redirects all output to a rule-specific log file when called by a Snakemake rule (#35, @kelly-sovacool). New function pool_taxon_counts() pools OTU counts at a particular taxonomic level (e.g. genus, phylum, etc.) to enable comparing analyses at different taxonomic resolutions, as seen in https://doi.org/10.1128/mbio.03161-21 (#37, @kelly-sovacool). New function calc_relabun() calculates OTU relative abundances (#38, @kelly-sovacool). New custom themes for ggplot2: theme_sovacool() (#39, @kelly-sovacool) theme_lucas() (#40, @sklucas) Full Changelog: https://github.com/SchlossLab/schtools/compare/v0.2.1...v0.3.
Automated preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, a...
Full Changelog: https://github.com/SansamLab/Cut_And_Run_Analysis_SnakeMake/compare/v0.0.2-alpha...v...
SnakeMAGs is a workflow to reconstruct prokaryotic genomes from metagenomes. The main purpose of Sna...
Fixes for API changes in ggplot2 v3.4.0 and tidyselect v1.2.0 (#42, #44, @kelly-sovacool). pool_taxo...
set_knitr_opts() now sets message to FALSE (#45, @kelly-sovacool). New function get_wildcards_tbl()...
This version uses mikropml v1.4.0. What's Changed Specify col_types for benchmarks CSV file by @kel...
Upgrade to Varlociraptor 3.1 (@johanneskoester) Best-practice formatting (@johanneskoester) Fixed re...
Full Changelog: https://github.com/SansamLab/Cut_And_Run_Analysis_SnakeMake/compare/v1.1.1...v1.1.
This release creates five different outputs from mRNA-seq reads: .html reports of the mRNA-seq fa...
Full Changelog: https://github.com/SansamLab/Cut_And_Run_Analysis_SnakeMake/compare/v1.1.2...v1.1.
Full Changelog: https://github.com/SansamLab/Cut_And_Run_Analysis_SnakeMake/compare/v1.0.0...v1.0.
<p>This archive contains the Snakemake workflow used to produce the results presented in the above m...
Added linkouts to VarSEAK (@FelixMoelder). Updated to newer tool versions in case of GATK base recal...
Full Changelog: https://github.com/SansamLab/Process_RepTiming_Snakemake/compare/v1.0.1...v1.0.
Full Changelog: https://github.com/SansamLab/Cut_And_Run_Analysis_SnakeMake/compare/v1.0.1...v1.1.
Automated preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, a...
Full Changelog: https://github.com/SansamLab/Cut_And_Run_Analysis_SnakeMake/compare/v0.0.2-alpha...v...
SnakeMAGs is a workflow to reconstruct prokaryotic genomes from metagenomes. The main purpose of Sna...
Fixes for API changes in ggplot2 v3.4.0 and tidyselect v1.2.0 (#42, #44, @kelly-sovacool). pool_taxo...
set_knitr_opts() now sets message to FALSE (#45, @kelly-sovacool). New function get_wildcards_tbl()...
This version uses mikropml v1.4.0. What's Changed Specify col_types for benchmarks CSV file by @kel...
Upgrade to Varlociraptor 3.1 (@johanneskoester) Best-practice formatting (@johanneskoester) Fixed re...
Full Changelog: https://github.com/SansamLab/Cut_And_Run_Analysis_SnakeMake/compare/v1.1.1...v1.1.
This release creates five different outputs from mRNA-seq reads: .html reports of the mRNA-seq fa...
Full Changelog: https://github.com/SansamLab/Cut_And_Run_Analysis_SnakeMake/compare/v1.1.2...v1.1.
Full Changelog: https://github.com/SansamLab/Cut_And_Run_Analysis_SnakeMake/compare/v1.0.0...v1.0.
<p>This archive contains the Snakemake workflow used to produce the results presented in the above m...
Added linkouts to VarSEAK (@FelixMoelder). Updated to newer tool versions in case of GATK base recal...
Full Changelog: https://github.com/SansamLab/Process_RepTiming_Snakemake/compare/v1.0.1...v1.0.
Full Changelog: https://github.com/SansamLab/Cut_And_Run_Analysis_SnakeMake/compare/v1.0.1...v1.1.
Automated preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, a...
Full Changelog: https://github.com/SansamLab/Cut_And_Run_Analysis_SnakeMake/compare/v0.0.2-alpha...v...
SnakeMAGs is a workflow to reconstruct prokaryotic genomes from metagenomes. The main purpose of Sna...