PopGenome
An Efficient Swiss Army Knife for Population Genomic Analyses

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335
Source code
151
Man pages
63
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PopGenome: An Efficient Swiss Army Knife for Population Genomic Analyses
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API

API for PopGenome
An Efficient Swiss Army Knife for Population Genomic Analyses

Global functions
Achaz.stats Man page
Achaz.stats,GENOME-method Man page
Achaz.stats-methods Man page
BayeScanR Man page Source code
D_jacknife Source code
DsDn Source code
F_ST.stats Man page
F_ST.stats,GENOME-method Man page
F_ST.stats-methods Man page
F_ST.stats.2 Man page
F_ST.stats.2,GENOME-method Man page
F_ST.stats.2-methods Man page
GENOME-class Man page
GFF_split_into_scaffolds Man page Source code
LOAD Source code
MK Source code
MKT Man page
MKT,GENOME-method Man page
MKT-methods Man page
MS Man page Source code
MS_getStats Man page Source code
MS_jointfreqdist Source code
PG_plot.biallelic.matrix Man page
PG_plot.biallelic.matrix,GENOME-method Man page
PG_plot.biallelic.matrix-methods Man page
PopGenome Man page Man page
PopGenread Source code
PopGplot Man page Source code
PsPn Source code
R2 Source code
VCF_split_into_scaffolds Man page Source code
Whop_readVCF Man page Source code
a1f Source code
a2f Source code
a2n Source code
an Source code
ap_calcR2 Source code
ap_pop Source code
ap_pop_FAST Source code
ap_pop_ancestral Source code Source code
b1f Source code
b2f Source code
calc.R2 Man page
calc.R2,GENOME-method Man page
calc.R2-methods Man page
calc.fixed.shared Man page
calc.fixed.shared,GENOME-method Man page
calc.fixed.shared-methods Man page
calcPi Source code
calcR2 Source code
calc_BD Source code
calc_Bd_CLR_table Source code
calc_Bd_clr Source code
calc_D Source code
calc_FS Source code
calc_RNDmin Source code
calc_average_nuc_diversity_between_per_site Source code
calc_df Source code
calc_diversities Source code
calc_freqstats Source code
calc_freqstats_FAST Source code
calc_hwhafsth Source code
calc_hwhafsth_FAST Source code
calc_miss Source code
calc_nuc_diversity_within Source code
calc_nuc_diversity_within_per_site Source code
calc_phi_st Source code
calc_pi Source code
calc_probabilities Source code
calc_quantile Source code
calc_sxsfss Source code
check_init_length Source code
checkpoppairs Source code
coalsim Source code
coalsimC Source code
codonise64 Source code
codontable Man page Source code
complike Source code
complike_FST Source code
compute_intern_achaz Source code
concatenate Source code
concatenate.classes Man page Source code
concatenate.regions Man page Source code
concatenate_to_whole_genome Source code
count.unknowns Man page
count.unknowns,GENOME-method Man page
count.unknowns-methods Man page
count_congruent Source code
counthaplotype Source code
create.PopGenome.method Man page Source code
create_SNP_matrix Source code
del Source code
delNULLpop Source code
deletecodongaps Source code
detail.stats Man page
detail.stats,GENOME-method Man page
detail.stats-methods Man page
diversity.stats Man page
diversity.stats,GENOME-method Man page
diversity.stats-methods Man page
diversity.stats.between Man page
diversity.stats.between,GENOME-method Man page
diversity.stats.between-methods Man page
ehh Source code
fasta_file Man page
fay_wu_normalized2 Source code Source code
fisherextest Source code
fitting_gff Source code
fitting_gff_fast Source code
fl_d Source code Source code
fl_d2 Source code Source code
fl_f Source code Source code
fl_f2 Source code Source code
freqtestn_achaz Source code
freqtesto_achaz Source code
fstcal Source code
fstcalc Source code
fuliF Source code
get.F_ST Man page
get.F_ST,GENOME-method Man page
get.F_ST-methods Man page
get.MKT Man page
get.MKT,GENOME-method Man page
get.MKT-methods Man page
get.biallelic.matrix Man page Source code
get.biallelic.matrix,GENOME-method Man page
get.biallelic.matrix-methods Man page
get.codons Man page
get.codons,GENOME-method Man page
get.codons-methods Man page
get.detail Man page
get.detail,GENOME-method Man page
get.detail-methods Man page
get.diversity Man page
get.diversity,GENOME-method Man page
get.diversity-methods Man page
get.feature.names Man page Source code
get.individuals Man page
get.individuals,GENOME-method Man page
get.individuals-methods Man page
get.linkage Man page
get.linkage,GENOME-method Man page
get.linkage-methods Man page
get.neutrality Man page
get.neutrality,GENOME-method Man page
get.neutrality-methods Man page
get.polymorph Source code
get.recomb Man page
get.recomb,GENOME-method Man page
get.recomb-methods Man page
get.status Man page
get.status,GENOME-method Man page
get.status-methods Man page
get.sum.data Man page
get.sum.data,GENOME-method Man page
get.sum.data-methods Man page
get.sweeps Man page
get.sweeps,GENOME-method Man page
get.sweeps-methods Man page
getBayes Man page
getBayes,GENOME-method Man page
getBayes-methods Man page
getDemographyParam Source code
getFREQanc Source code Source code
getMS,GENOME-method Man page
getTable Source code
get_data Source code
get_fixed_shared Source code
get_freq Source code
get_gff_info Man page Source code
get_monomorph Source code Source code
get_outgroup Source code Source code
get_ref_alleles Source code
get_segsites Source code
get_segsites_FAST Source code
get_sfreqh Source code
getsyn Source code
getsynnonsyndiff_my Source code
gffRead Source code
gff_file Man page
gtest Source code
haplochi2 Source code
hudsonkaplan85rm Source code
i_codonsynnonsyn2 Source code
i_countSynNonsynDiff Source code
import_file Source code
intern.calc.R2 Source code
introgression.stats Man page
introgression.stats,GENOME-method Man page
introgression.stats-methods Man page
is.wholenumber Source code
ispolmisX Source code
jack.knife.transform Man page
jack.knife.transform,GENOME-method Man page
jack.knife.transform-methods Man page
jointfreqdist Source code
jump_model_codominant Source code
linkage.stats Man page
linkage.stats,GENOME-method Man page
linkage.stats-methods Man page
linkdisequ Source code
linkdisequ_FAST Source code
load.session Man page Source code
log_prior_alpha Source code
mismatch Source code
mktest Source code
mult.linkage.stats Man page
mult.linkage.stats,GENOME-method Man page
mult.linkage.stats-methods Man page
myReadVCF Source code
my_chunk Source code
my_read.nexus Source code
my_unique Source code
neutrality.stats Man page
neutrality.stats,GENOME-method Man page
neutrality.stats-methods Man page
omegai Source code
omegain Source code
pair_linkdisequ Source code
pair_linkdisequ_FAST Source code
parse_HapMap Source code
parse_gff Source code
plot_avg_cs Source code
popFSTN,GENOME-method Man page
popGetBial Source code
popgen Source code
progressDots Source code
psii Source code
read.big.fasta Man page Source code
read.big.ms.output Source code
read.ms.output Source code
readData Man page Source code
readHapMap Man page Source code
readMS Man page Source code
readSNP Man page Source code
readVCF Man page Source code
readVCFchunk Source code
readVCFchunkHap Source code
readVCFchunk_tet Source code
readVCFchunk_tri Source code
recomb.stats Man page
recomb.stats,GENOME-method Man page
recomb.stats-methods Man page
region.as.fasta Man page
region.as.fasta,GENOME-method Man page
region.as.fasta-methods Man page
rhoij Source code
save.session Man page Source code
set.filter Man page
set.filter,GENOME-method Man page
set.filter-methods Man page
set.outgroup Man page
set.outgroup,GENOME-method Man page
set.outgroup-methods Man page
set.populations Man page
set.populations,GENOME-method Man page
set.populations-methods Man page
set.ref.positions Man page
set.ref.positions,GENOME-method Man page
set.ref.positions-methods Man page
set.synnonsyn Man page
set.synnonsyn,GENOME-method Man page
set.synnonsyn-methods Man page
set_gff_info Source code
show,GENOME-method Man page
show.slots Man page
show.slots,GENOME-method Man page
show.slots-methods Man page
sigmaii Source code
sigmaij Source code
site_FST Source code
site_diversity_between Source code
sliding.window.transform Man page
sliding.window.transform,GENOME-method Man page
sliding.window.transform-methods Man page
snn Source code
snp_file Man page
split.GFF Source code
split_data_into_GFF_attributes Man page Source code
split_data_into_GFF_features Man page Source code
splitting.data Man page
splitting.data,GENOME-method Man page
splitting.data-methods Man page
stirling Source code
sweeps.stats Man page
sweeps.stats,GENOME-method Man page
sweeps.stats-methods Man page
tajimaD Source code
test.params Man page
test.params-class Man page
thetaH Source code
tn93 Source code
update_d_alphaco_i Source code
update_d_betaco Source code
update_freq_codominant Source code
usage,GENOME-method Man page
vcf_file Man page
wall99bq Source code
weighted.jackknife Man page
weighted.jackknife,GENOME-method Man page
weighted.jackknife-methods Man page
PopGenome documentation built on Feb. 1, 2020, 1:07 a.m.

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