vjcitn

library(GenomicState)
library(RSQLite)
library(txdbmaker)
hgenc49 = gencode_txdb(
       version = "49",
       genome = c("hg38"),
       chrs = paste0("chr", c(seq_len(22), "X", "Y", "M"))
     )
hgenc49$conn  # 'path' is empty
md = dbGetQuery(hgenc49$conn, "select * from metadata")  # lacks 'Resource URL' record in metadata

vjcitn

8/51 [install-miniconda]
  trying URL 'https://github.com/conda-forge/miniforge/releases/latest/download/Miniforge3-Linux-x86_64.sh'
  Content type 'application/octet-stream' length 105158150 bytes (100.3 MB)
  ==================================================
  downloaded 100.3 MB
  
  PREFIX=/root/.local/share/r-miniconda
  Unpacking bootstrapper...
  Unpacking payload...
  Extracting _libgcc_mutex-0.1-conda_forge.tar.bz2

vjcitn

> query(ah, c("GENCODE", "human"))
AnnotationHub with 87 records
# snapshotDate(): 2025-10-29
# $dataprovider: GENCODE, Gencode, BroadInstitute, ENCODE
# $species: Homo sapiens
# $rdataclass: GRanges, list, TxDb, SQLiteConnection
# additional mcols(): taxonomyid, genome, description,
#   coordinate_1_based, maintainer, rdatadateadded, preparerclass, tags,
#   rdatapath, sourceurl, sourcetype 
# retrieve records with, e.g., 'object[["AH49010"]]' 

vjcitn

library(DelayedArray)

setClass("plBedSeed",
  contains="Array",
  slots = c(
   dim = "integer",
   bedreaderRef = "ANY",
   dimnames = "list"
   )
)

vjcitn

make1zip = function(pname, target="zips322") {
 if (!dir.exists(target)) dir.create(target)
 target = file.path(getwd(), target)
 ins = try(BiocManager::install(pname, ask=FALSE, update=FALSE, type="binary", 
                                dependencies=TRUE, force=TRUE)) # acquire dependencies as needed
 if (inherits(ins, "try-error")) stop(sprintf("can't install %s with BiocManager", pname))
 #real_inst = try(install.packages(pname, type="source", repos=NULL))  # this uses native windows build tools from Rtools
 bpath = pkgbuild::build(pname)
 if (inherits(bpath, "try-error")) stop(sprintf("can't build %s from source", pname))
 install.packages(bpath, type="source", repos=NULL)

vjcitn

library(BiocPkgTools)
all322 = biocPkgList(version="3.22", repo="BioCsoft")$Package
library(BiocBuildTools) # from github vjcitn
set322=PackageSet(all322, biocversion="3.22", branchname="RELEASE_3_22")
dir.create("srcs_322")
populate_local_gits(set322, gitspath="srcs_322")

vjcitn

from owlready2 import get_ontology, onto_path, sync_reasoner

def find_terms_by_keyword(ontology, keyword):
    # Simple case: search class labels and names
    results = []
    for cls in ontology.classes():
        label = cls.label.first() if hasattr(cls, "label") and cls.label else cls.name
        if keyword.lower() in label.lower():
            results.append(cls)
    return results

vjcitn

from owlready2 import get_ontology, onto_path
import numpy as np

def term_to_class(user_term, onto):
    all_terms = list(onto.classes())
    excluded_terms = get_excluded_terms(onto)
    # Try to find by label first, then by name
    found = None
    for cls in all_terms:
        if cls in excluded_terms:

vjcitn

library(SummarizedExperiment)
library(irlba)
ibiplot = function(se, choices=1:2, nfeat=5, ircomp=6, ...) {
  dat = t(assay(se))
  pcs = prcomp_irlba(dat, ircomp)
  rot = pcs$rotation
  ss = rowSums(abs(rot[,choices])^2)
  kp = order(ss, decreasing=TRUE)[seq_len(nfeat)]
  labs = rep(" ", nrow(rot))
  labs[kp] = rownames(se)[kp]

vjcitn

library(S4Vectors)
library(SummarizedExperiment)
library(GDSArray)
library(bigmelon)
data(melon)
tf = tempfile()
es2gds(melon, tf)

bm2SE = function(gdsf, elem="betas",
    fdkeep=c("ProbeID_A", "ProbeID_B", "ILMNID", "NAME",