A set of processes/pipelines for bioinformatics
Bot releases are hidden (Show)
Full Changelog: https://github.com/pwwang/biopipen/compare/0.31.7...0.32.0
Published by pwwang 2 months ago
biopipen/**/*.py
Full Changelog: https://github.com/pwwang/biopipen/compare/0.31.6...0.31.7
Published by pwwang 2 months ago
Full Changelog: https://github.com/pwwang/biopipen/compare/0.31.5...0.31.6
Published by pwwang 2 months ago
Full Changelog: https://github.com/pwwang/biopipen/compare/0.31.4...0.31.5
Published by pwwang 3 months ago
Full Changelog: https://github.com/pwwang/biopipen/compare/0.31.3...0.31.4
Published by pwwang 3 months ago
Full Changelog: https://github.com/pwwang/biopipen/compare/0.31.2...0.31.3
Published by pwwang 3 months ago
Full Changelog: https://github.com/pwwang/biopipen/compare/0.31.1...0.31.2
Published by pwwang 3 months ago
Full Changelog: https://github.com/pwwang/biopipen/compare/0.31.0...0.31.1
Published by pwwang 3 months ago
Full Changelog: https://github.com/pwwang/biopipen/compare/0.30.0...0.31.0
Published by pwwang 3 months ago
SeuratClustering/SeuratSubClustering
to SeuratClusterStats
envs.skip_if_normalized
option to skip normalization if query is already normalized using the same method as the referenceSeuratClustering
and SeuratSubClustering
envs.create_bam
not working for cellranger v7plugin_opts.poplog_max
envs.tool
for Download/DownloadListMetaPvalue
and MetaPvalue1
Full Changelog: https://github.com/pwwang/biopipen/compare/0.29.2...0.30.0
Published by pwwang 4 months ago
PrepSCTFindMarkers
when necessary before calling meta-markersFull Changelog: https://github.com/pwwang/biopipen/compare/0.29.1...0.29.2
Published by pwwang 4 months ago
regulation
to regulatory
envs.title
to None
(don't add title to the plot by default)envs.ylabel
not workingMediation
for mediation analysis--keep-allele-order
to keep the allele ordereach
is specified.each
is specifiedPrepSCTFindMarkers
when necessary before calling FindMarkersdoubletfinder
to run with a different number of coresPrepSCTFindMarkers
command in sobj@commands
doubletfinder
in testsFull Changelog: https://github.com/pwwang/biopipen/compare/0.29.0...0.29.1
Published by pwwang 4 months ago
pipen-filters
to version 0.13meme
to env_bio.yml
for testsPlinkFromVcf
to convert VCF files to PLINK formatPlink2GTMat
for converting PLINK files to genotype matrixPlinkIBD
analysis for identity by descentPlinkHWE
for Hardy-Weinberg Equilibrium testPlinkHet
for calculating sample heterozygosityPlinkCallRate
for calculating call rate of samples and variantsPlinkFilter
process for filtering PLINK filesPlinkFreq
process for calculating and filtering by allele frequenciesPlinkUpdateName
proc to update variant names in PLINK filesGenePromoters
for retrieving gene promoter regions and tests for itBedtoolsIntersect
process for finding the intersection of two BED filesMotifScan
to use fimo for motif scanningMotifAffinityTest
to test the affinity of motifs to the sequences and the affinity change due the mutations.envs.ref
in mulitple processesManhattanPlot
to for support for plotting Manhattan plotsQQPlot
proc for generating QQ-plot or PP-plotBcftoolsView
process for viewing, subsetting, and filtering VCF filesrun_bcftools
function for running bcftools with given argumentsMetaPvalue1
to combine pvalues from the same fileenvs.keep_single
flag to keep the single p-valuesrun_command
function for Rtabix_index
to index infile directlygene_name_conversion
functions for both python and Rin.name
envs.notfound
to be ignore
or skip
when envs.output
is append
or replace
run_command
functionrun_command
functiongene_name_conversion
biopipen-r
bioconductor-ggmanh
dependency to version 1.9.6envs.model
tabix_index
function-f
to bgzip or gunzip to overwrite the output if existsenvs.shared_clusters.heatmap_meta
being broken by envs.shared_clusters.sample_order
envs.use
or values of envs.MapQuery.refdata
not in referenceFindClusters
to run for multiple resolutionsFindClusters
to run for multiple resolutionsFull Changelog: https://github.com/pwwang/biopipen/compare/0.28.1...0.29.0
Published by pwwang 5 months ago
CellTypeAnnotation
using scCATCH
envs.create_bam
to control whether create bams (supporting cellranger v8)in.id
to CellRangerCount
and CellRangerVdj
to specify sample idsreport_paging
to 8Full Changelog: https://github.com/pwwang/biopipen/compare/0.27.9...0.28.0
Published by pwwang 5 months ago
sample_order
to set sample order on heatmap and cluster_rows
to switch row clustering on/offFull Changelog: https://github.com/pwwang/biopipen/compare/0.27.8...0.27.9
Published by pwwang 5 months ago
Full Changelog: https://github.com/pwwang/biopipen/compare/0.27.7...0.27.8
Published by pwwang 5 months ago
runFGSEA
do_one_group
and save a warning file under the caselocalizeGmtfile
prep_reference.py
Full Changelog: https://github.com/pwwang/biopipen/compare/0.27.6...0.27.7
Published by pwwang 5 months ago
do_one_group
runFGSEA
pipen.run()
to test the successFull Changelog: https://github.com/pwwang/biopipen/compare/0.27.5...0.27.6
Published by pwwang 5 months ago
envs.cell_qc_per_sample
to filter cells before merging instead afterFull Changelog: https://github.com/pwwang/biopipen/compare/0.27.4...0.27.5