Man pages for thierrygosselin/stackr
Run stacks software pipeline for RADseq analysis inside R

build_stackr_workflow_dirBuild stacks workflow directories
change_pop_namesTransform into a factor the POP_ID column, change names and...
check_fqcheck_fq
clean_fqRemoves the noise of an individual fastq file
clean_fq_filenameclean_fq_filename
clean_ind_namesclean individual's name
clean_markers_namesClean marker's name
clean_pop_namesClean population's name
compound_assignment_pipe_operatorcompound assignment pipe operator
Exposition_pipe_operatorExposition pipe-operator
extract_catalog_sql_idsExtract sample SQL IDs from STACKS catalog file
fq_file_typefq_file_type
list_sample_filelist_sample_file
loc_pop_statsloc_pop_stats
merge_bammerge_bam
merge_fqmerge_fq
merge_parallelmerge_parallel
mismatch_dirGenerate mismatch directory
mismatch_figmismatch_fig
nThe number of observations in the current group.
normalize_readsRarefaction of reads samples
pipi
pipeForward-pipe operator
pi_poppi_pop
read_counterCounts the number of reads in samples
read_count_oneread_count_one
read_depth_plotGenerate a figure with the read depth groups
reads_length_distributionGenerate the read length distribution of a fastq file
reads_statsreads_stats
read_stacks_ustacks_logRead stacks ustacks log
rename_fqRename fastq files
run_cstacksRun STACKS cstacks module
run_gstacksRun STACKS new module called gstacks
run_populationsRun STACKS Version >= 2.0 populations module
run_process_radtagsRun STACKS process_radtags module
run_radprocRun RADproc
run_split_cstacksrun_split_cstacks
run_sstacksRun STACKS sstacks module
run_tsv2bamRun STACKS tsv2bam and merges BAM files
run_ustacksRun STACKS ustacks module
run_ustacks_one_samplerun_ustacks_one_sample
separate_haploseparate_haplo
separate_haplo_longseparate_haplo_long
split_bam_listsplit_bam_list
split_pop_mapsplit_pop_map
split_tibble_rowssplit_tibble_rows
split_vec_rowsplit_vec_row
stackr_normalizestackr_normalize
stackr_parallelhack to switch function for parallel computation based on OS
stats_stackrstats_stackr
strata_haplostrata_haplo
summary_catalog_log_likSummary of catalog log likelihood
summary_cstacksSummarize STACKS cstacks log file generated by stackr
summary_genotypesSummary of 'batch_x.genotypes.txt' and 'batch_x.markers.tsv'...
summary_haplotypesHaplotypes file summary
summary_pstacksSummarize STACKS pstacks files
summary_readsSummarise the reads for indel and GC content and produce the...
summary_sstacksSummarize STACKS sstacks log file generated by stackr
summary_ustacksSummarize STACKS ustacks files
write_normalizewrite_normalize
thierrygosselin/stackr documentation built on Nov. 11, 2020, 11 a.m.