NEWS.md

sigminer 2.3.1

sigminer 2.3.0

get_sig_db("latest_RNA-SBS_GRCh37")
get_sig_db("latest_SV_GRCh38")

sigminer 2.2.2

Example:

load(system.file("extdata", "toy_mutational_signature.RData",
                 package = "sigminer", mustWork = TRUE
))
# Show signature exposure
p1 <- show_sig_exposure(sig2, rm_space = TRUE)
p1

expo = sig_exposure(sig2)
show_sig_exposure(expo,
                  rm_space = TRUE,
                  samps = colnames(expo)[order(colSums(expo))])

sigminer 2.2.1

sigminer 2.2.0

sigminer 2.1.10

sigminer 2.1.9

sigminer 2.1.8

sigminer 2.1.7

sigminer 2.1.6

sigminer 2.1.5

Example:

set.seed(1234)
df <- dplyr::tibble(
  g1 = rep(LETTERS[1:3], c(50, 40, 10)),
  g2 = rep(c("AA", "VV", "XX"), c(50, 40, 10)),
  e1 = sample(c("P", "N"), 100, replace = TRUE),
  e2 = rnorm(100)
)

x1 = group_enrichment(df, grp_vars = c("g1", "g2"), 
                      enrich_vars = c("e1", "e2"), 
                      ref_group = c("B", "VV"))
x1

sigminer 2.1.4

sigminer 2.1.3

sigminer 2.1.2

sigminer 2.1.1

sigminer 2.1.0

sigminer 2.0.5

sigminer 2.0.4

sigminer 2.0.3

sigminer 2.0.2

sigminer 2.0.1

sigminer 2.0.0

BUG REPORTS

ENHANCEMENTS

for (i in c("latest_SBS_GRCh37", "latest_DBS_GRCh37", "latest_ID_GRCh37",
            "latest_SBS_GRCh38", "latest_DBS_GRCh38",
            "latest_SBS_mm9", "latest_DBS_mm9",
            "latest_SBS_mm10", "latest_DBS_mm10",
            "latest_SBS_rn6", "latest_DBS_rn6")) {
  message(i)
  get_sig_db(i)
}

NEW FUNCTIONS

DEPRECATED

sigminer 1.2.5

BUG REPORTS

ENHANCEMENTS

NEW FUNCTIONS

DEPRECATED

sigminer 1.2.4

BUG REPORTS

ENHANCEMENTS

NEW FUNCTIONS

DEPRECATED

sigminer 1.2.2

BUG REPORTS

ENHANCEMENTS

NEW FUNCTIONS

DEPRECATED

sigminer 1.2.1

BUG REPORTS

ENHANCEMENTS

NEW FUNCTIONS

DEPRECATED

sigminer 1.2.0

BUG REPORTS

ENHANCEMENTS

NEW FUNCTIONS

DEPRECATED

sigminer 1.1.0

sigminer 1.0.19

sigminer 1.0.18

sigminer 1.0.17

sigminer 1.0.16

sigminer 1.0.15

sigminer 1.0.14

sigminer 1.0.13

sigminer 1.0.12

sigminer 1.0.11

sigminer 1.0.10

sigminer 1.0.9

sigminer 1.0.8

sigminer 1.0.7

sigminer 1.0.6

sigminer 1.0.5

sigminer 1.0.4

sigminer 1.0.3

sigminer 1.0.2

sigminer 1.0.1

sigminer 1.0.0

All users, this is a break-through version of sigminer, most of functions have been modified, more features are implemented. Please read the reference list to see the function groups and their functionalities.

Please read the vignette for usage.

I Hope it helps your research work and makes a new contribution to the scientific community.



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sigminer documentation built on May 29, 2024, 3:11 a.m.