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Open Source Biology & Genetics Interest Group

Open source scripts, reports, and preprints for in vitro biology, genetics, bioinformatics, crispr, and other biotech applications.

 Posted in Research

Kenya is emerging as a major hub of CRISPR biomedical research in Africa

 August 12, 2021

Kenyan scientist Dr Hussein Abkallo wound up in the sophisticated world of Crispr Cas9 almost by chance, unaware that the decision would catapult …

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Tagged cas9, crispr

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EMBL Australia Group Leader in neural regeneration and/or organ engineering and synthetic biology →
← proportion of variance

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.bbs .bim .csv .evec .faa .fam .Gbk .gmt .NET Bio .PDBQT .tar.gz 23andMe A375 ABEs ABL-21058B ACADVL AccuraDX ACE2 aCGH ACLAME ACTB ACTREC addgene ADMIXTURE Adobe Audition adonis ADPribose AF AfterQC AGAT AI-sandbox ajax AJOU Alaskapox ALCL ALDEx2 Alevin ALK ALOT AlphaDesign AlphaFold ALS AML AMOS AMP AMPHORA Ampure XP Amyloidosis Anaconda ancestryDNA ANCOM-BC ANGeS ANGPTL8 ANGSD anitaokoh annotateMyIDs AnnotationDbi annotationHub annovar ANSYS anti-aliasing anti-BCMA Anti-PD-1 antiSMASH Apache Kafka APC apex apollo ARACNE-AP ArcGIS Arduino arm64 ARRmNormalization Ascalaph Designer ASM212806v1 ASM238634v1 ASM287662v1 ASM298219v1 ASM314399v1 ASM350094v1 ASM1227490v1 ASoC aspera ASVs ATAC ATAC-SEQ ATCC ATG ATM atpB-rbcL ATTR AutoDock AutoML AUTOR Avogadro AZ BAC BALB BAM bamdst barplot baseml bash BATF3 BattleMetrics BBDuk BBMap BBMerge BBTools BCFtools bcl2fastq BCR bdgcmp beagle BEAST BED bedGraph BEDtools bfiles BGCs bgen BGmix BiGG bigWig bin Bing Bio-DB-HTS BiocGenerics Bioclipse 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config.txt ConsensusClusterPlus Control-FREEC CookHLA corr.test COSMIC CP033719 CP2K CpG Cr2O3 cram cran CRIMS CRISPOR crispr CRISPRa CRISPRko CRLMM cRNA CROP-seq crRNA CRyPTIC CSI ctDNA cto Cutadapt CWL CXCR4 cygwin CYP2D6 Cytochrome CyTOF cytoscape CyVerse DADA2 DAPARS2 darkRP DAW dba.plotProfile DBHI DBMR dbNSFP dCas9 dCas9-vp64 dCas9-VPR ddATP DdCBE-mediated ddCTP ddGTP ddH2O ddTTP DE-analysis DE-kupl decay DECIPHER deepTools DEG degradome-seq DEL Demovir DESC DESE2 DESeq deseq2 DGE dgelist diagnostic DiffBind directx Diva Django DLBCL DMR DMRs DMSO DNA DNA-seq DNAseq dnasp dNdScv DoBISCUIT DOCK2 docker dplyr DRG DRIMseq DROP-seq DSB dsDNA dseq2 dsQTL dsRed dtu DuoClustering2018 EB Eclipse IDE EcoR1 EDTA EdU eGFP-Puro EggNOG egsea EGT2 EHMT2 eisa electrotransfection ELN EMBL EMBL-EBI EMBOSS ENA eNeuro enformer enhancedVolcano ENmix enrichGO enrichkegg enrichr ENSCAFG1 ensembl ENSEMBL ID ENSG entrezID EOF EpCAM EPN eQTL ER-lysosome ERA ers ERSSA ESBL-EC eureKARE eureKAWARDS ex-psu exceRpt ExPASy FACS FAIR FAP FAQs FAST5 FASTA fasterq-dump fastp fastq fastQC FASTY FBXW7 fcScan FDA fData featureSet feature_db FEBS fetchChromSize ffmpeg FGFR2 FGFR3 Ficoll file.ht2 fimo findMotifsGenome.pl Finite Element Method flagstat Flavivirus-GLUE flowStats flowTrans FoldGO FPKM fq.gz FreeBayes FreeBSD FRiP FSHD FunciSNP G2Net Gag/Pol GAM GAPDH gaschYHS GATK gBlock GBM GBR GBS GC GC-content GCA gcta GDAC gDNA GeCKO GEDmatch geecc GeForce GTX gemBS GEMMA GenBank genblastA Gene-Ontology GeneDX GeneGA geneID geneMANIA GenePattern GeneRfold GenGIS genome-wide genomeGenerate GenomeInfoDb genomelink genomeLoad Genomespace GenomeStudio genomic genomica GenomicsDBImport GENtle Gentoo GenXys GEO GEO2R GEOexplorer GEOquery GEO_OPT getEAWP getfasta getGEO Geworkbench GEX GFF gff3 gffread GFP ggalt GGBase GGG gGmbH ggplot ggplot2 GGtools ggtree GIAB GISTIC GISTIC2.0 github gitlab gja5 glmLRT global25 GM12891 GM12892 GMOD gnomAD gnomADc gnomix GNU GOChord GOI golubEsets GOPATH GOrilla GOSemSim GOseq GPL Grain GraphQL GRCH37 GRCH38 GRCm38 GRCm39 grenits GREP GRM gRNA GROMACS grompp GRRDUser GSA GSE66099 GSE172016 GSEA gseGO gsekegg GSM-SAMPLES GSTAr,GSTA Gstreamer gsva GTA gtex gtf GtRNAdb GUI GUIDANCE GWAS GWASpower H3K9me3 H3K27ac H5AD H2122 haplogroup s HaplotypeCaller haplotypes HCC HDCytoData HDMI HDR HDR-CRISPR heatmaps HEK293 HEK293T HeLa HepG2 hg19 hg38 HGNC HGT HGU133Plus2 HiC-Pro HiFiBiO HilbertVis hiPSCs hisat2 hiSeq HiTC HitTable HMM hmmer Hmox1 HNC homeoboxB9 HOMER HPC HPC-reditools HPLC HPV HR HRS hs37d5 HT-Seq HTqPCR HTseq HTSeq-count HTSlib HuGene-1_0-st HVS HYBRID hypergravitropic I-TASSER IC50 ICA ICAR ICheckpointHelperClient iCOMIC IDbyDNA IDR IEEE IgG IGM ignoreTxVersion IGV IJMS IL-2R ILMN ImdSession Impl IMPUTE2 IncRNA indel InferCNV iNMF install.packages IntegraGen Integrated Genome Browser InterMine InterPro InterProScan intronsByTranscript IOError ION torrent IP-MS ipdsummary iPSC iPSCs IRI ischemia-reperfusion ISD iseq iso-seq iTOL IVT JASPAR Java javascript jbrowse jobRxiv Jquery json JSON Schema JunctionSeq junk DNA Jupyter jupyterhub K-mer k-smoothing K562 kaggle KaryoploteR kegg Kernel KeyError Kibana kissplice KO Kraken2 KRAS KRASG12C KSpace kubectl kubernetes L2FC L4D2 label_format LABGeM LabKey Server LAMMPS LAMP LaTeX LD LDDT LEfse LentiCRISPR LentiCRISPRv2 leukocyt libgromacs5 Liftoff ligand-interaction LIMMA LIMS LiP-MS LIU LLC lme4 LMGene lncRNA locus_tag LoF log2FoldChange logCPM logFC Logic LRRK2 lumiHumanIDMapping LwaCas13a Lynch LZMA m10kcod.db MACS macs2_bdgdiff MAFFT MAGeCK MAGs maizeprobe Makeblastdb MALT MAplot MAPQ MarkduplicatesSpark marr MARS-seq MashupMD matplotlib MBEDTLS MCF10A mcr-1 mCRC mCRPC MCScanX MD MDS MECP2 medulloblastoma mega-x Megahit melanoma MemVerge MergeSamFiles mESC mESCs MeSH.Pto.eg.db MetaCyc Metagenome MetaGxPancreas MetaPhlAn2 MetaProdigal metawrap METHPED MethylationEPIC methylclockData methylkit MetID MG-rast mg1655 MGEs MHC-I MIC-Drop MicroGenDX mig minimap2 MinION MINSEQE miQC MiRBase mirdeep2 miRNAseq MISeq mixcr mkref MLE MMBIR MMR mnp modelr MOFA MoGene-1_0-st-v1 MOI mol MongoDB monocle2 monocle3 monoclle3 montana Monterey mothur motIV Mpeg MPH mphil mpileup mps MQTT MRC MRD mRNA MRSA msa msc MSGFgui MSI MSigDB msk MSMC MTB mtDNA MTHFD1 multi-omic MULTI-seq MUMmer mummerplot MuTect MUTECT2 MXene MYC mydb MYO10 MySQL NA NAMESPACE NAR NBAMSeq nc1700sJORDAN ncbi NCC NCFamilyGenetic ncRNA NEB neofart netbenchmark NetCoMi netprioR NewStem next-gen Next.js NextDenovo nextflow Nextseq Nexus nf-core NFDI4Microbiota NfL NGG nginx NGS NGS-Lib-Fwd NHEJ NHS NIH NLS Node.js NovaSeq NovelStem NPC NPSR1 nr NTLA nu Nucleosome NUMTS NuProbe NVIDIA odseq OMA omic OMIM ONT oocyte openAPI OpenKIM OpenMP openSUSE OpenWrt orf OTU OVCAR3 p53 pA PacBio PACR pact_00210 PAIRADISE pairwise2 PARPis PASS PATCH v2 pathfindR PathVisio pax3 pbs PCA PCR pd.hg.focus PDAC pData pdb PDBE pdInfoBuilder PedPhase pegRNAs PERMANOVA perTargetCoverage Pfam pgdx PGGB PGS phase_trio.sh phastConsElements phd pheatmap phenix PhiX Phoenix PHRED phyloseq Phylum PI3 picard PICS PIK3CA PIM Pindel platypus pLentiCRISPRv2 plink plotMA PLS-DA POLG1 polyphen2 PopGen PopGenome popmax PostgreSQL PowerBI PPI ppinfer PrCa pre-IPO PredicineCARE primer3 PrognomiQ Promethease PROPER-seq ProteoDisco provean PRS PRSice PRSice-2 pseudotime psgendb psiblast PSMC Psme1 pSpCas9 psyt PTM PubMed pUC19 pULA105E PuTTY px459 Pybedtools PyCharm pyHAM PYMC3 pymol pymolrc python PythonRepo pytorch QA QC qctool v2 Qiagen QIAseq QIIME2 qPCR qqplot QUAL qualimap quant.sf Quanta Quantseq query R r-bioc-basilisk r-bioc-deseq2 rabbitmq RACK1 RAD-seq ragdolls ramr ranzcr RASMOL raw_counts RBPs RCB RCorrector RDAVIDWebService RDocumentation reactjs reactome.db ReactomePA ReadAffy readDGE readDNAStringSet recount2 recovery REditools2 RefSeq regex RegExp relatedness resonance REVIGO RFLP RFM RFP RFS RfxCas13d RGBA rgsepd RIMS-seq RINalyzer rip-md RIPSeekerData rlogTransformation RMA RNA RNAmodR.Data RNAseP RNAseq rnaturalearth rnaturalearthdata roblox ROH RPKM rpoB RPPA RQN RRBS RRHO2 rRNA RSEM RSeQC rsIDs RSQLite Rstudio Rsubread RT-qPCR RTMP rtracklayer rTRMui Ruby RUnit RUNX2 rust-bio S4Vectors SageMath sagenome SAIGE Salmon SAM sambamba samblaster SAMD9 sample samtool SAMtools SBS SBT ScarHRD scATAC-SEQ SCF SCID ScienceDaily SCIRP SCO-012 scRNA scRNAseq scVelo SCVI SED segemehl selenium seq-lang Seqio.Parse SeqIO.pm Serum SEs Seurat SFS sgRNA Shapeit shell Shiny shRNA sift SILVA Single.mTEC.Transcriptomes SingleR SingscoreAMLMutations sjdbOverhang SKAT-O SKCM SLURM SMAD4 smallRNA smallRNAseq SMAP smartPCA SmartSeq SMRT SNAKEMAKE snap snoRNP snp SnpEff SNPRelate snpsift snRNA-seq snsplot SNV SOAP SOAP Suite SOS SPAdes SpCas9 Spike-Ins SPSS SQL SQLite SRA sra-toolkit SRC SRF SRP SRR ssDNA SSL ssRNA Stackify Staden Package STAR stats4 Steam stem STP StrainPhlAn stref_00240 StringTie sv SV40 SwissProt Synapse Syntekabio Synths systemPipeRdata T7RNAP TAIR tblastx TBSignatureProfiler TCC 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Videos

European Bioconductor Conference 2022 Live Stream from Heidelberg, Germany (talks only) https://eurobioc2022.bioconductor.org/schedule/ 09:00 Keynote Dr. Björn Grüning: Developing interoperable frameworks for the scientific community 09:45 Flashtalks 10:30 Coffee break 11:00 Special session Birds-of-a-Feather, Three parallel sessions 12:00 Lunch 13:00 Special session Birds-of-a-Feather, Three parallel sessions 14:30 Coffee break 14:50 End of Day 3 Closing remarks
EuroBioC2022 Live Stream Day 3: morning
European Bioconductor Conference 2022 Live Stream from Heidelberg, Germany (talks only) https://eurobioc2022.bioconductor.org/schedule/ 16:20 Short talk Short talk 19: DifferentialRegulation: a novel approach to identify differentially regulated genes. Simone Tiberi 16:30 Short talk Short talk 20: Analysis of transposable elements in R and Bioconductor with atena. Beatriz Calvo-Serra 16:40 Short talk Short talk 21: Inclusive instruction in cancer data science: Authoring and deployment with yes4cure. Alexandru Mahmoud
EuroBioC2022 Live Stream Day 2: afternoon
European Bioconductor Conference 2022 Live Stream from Heidelberg, Germany (talks only) https://eurobioc2022.bioconductor.org/schedule/ 14:35 Keynote Dr. Michael Dorrity: Developmental robustness of zebrafish embryos at single-cell resolution
EuroBioC2022 Live Stream Day 2: noon
European Bioconductor Conference 2022 Live Stream from Heidelberg, Germany (talks only) https://eurobioc2022.bioconductor.org/schedule/ 09:15 Keynote Dr. Judith Zaugg 10:00 Coffee break 10:10 Short talk Short talk 8: Smooth epigenomics data analysis and visualisation with Bioconductor (or: an ode to Rle). Pierre-Luc Germain 10:20 Short talk Short talk 9: MethQuant: A package providing entropy-based measures for quantifying patterns of DNA methylation heterogeneity in (single-cell) bisulfite sequencing data. Emanuel Sonder 10:30 Short talk Short talk 10: DeeDee - Evaluating, Visualizing, and Integrating Results from Differential Expression Analysis Workflows. Federico Marini 10:40 Short talk Short talk 11: Analysing multiplexed assays of variant effects with mutscan. Michael Stadler 10:50 Short talk Short talk 12: Joint modeling of rare variant genetic effects using deep learning and data-driven burden scores. Brian Clarke 11:00 Coffee break 11:30 Short talk Short talk 13: spillR: Causal Modelling of Spillover in Mass Cytometry. Marco Guazzini 11:40 Short talk Short talk 14: Multi-omic integration with cosmosR and ocEAn to study cross-talks between signalling and metabolism in diseases. Aurelien Dugourd 11:50 Short talk Short talk 15: A new principled approach for single-cell proteomics data analysis. Laurent Gatto 12:00 Short talk Short talk 16: Analyzing hydrogen-deuterium exchange mass-spectrometry data in R. Oliver Crook 12:10 Short talk Short talk 17: CTexploreR, a package to explore CT genes. Axelle Loriot
EuroBioC2022 Live Stream Day 2: morning
European Bioconductor Conference 2022 Live Stream from Heidelberg, Germany (talks only) https://eurobioc2022.bioconductor.org/schedule/ 14:10 Keynote Dr. Julio Saez-Rodriguez: Combining multi-omics data and biological knowledge to extract disease mechanisms
EuroBioC2022 Live Stream Day 1: afternoon
European Bioconductor Conference 2022 Live Stream from Heidelberg, Germany QUESTIONS: www.slido.com #1680070 (talks only) https://eurobioc2022.bioconductor.org/schedule/ 09:15 Introduction Welcome, Bioconductor overview, and Code of Conduct 09:40 Keynote Dr. Shila Ghazanfar: Integrative analyses for spatial genomics data 10:25 Break 10:30 Short talk Short talk 1: Co-clustering of Spatially Resolved Transcriptomic Data. Andrea Sottosanti 10:40 Short talk Short talk 2: Simplified, strand aware and comprehensive splicing analysis using IntEREst (1.22.0). Ali Oghabian 10:50 Short talk Short talk 3: Differential embedding analysis of multi-condition single-cell datasets. Constantin Ahlmann-Eltze 11:00 Coffee break 11:30 Short talk Short talk 4: Clinical microbiome data science with MultiAssayExperiment. Tuomas Borman 11:40 Short talk Short talk 5: µSTASIS - Assessment of human microbiota stability across longitudinal samples. Pedro Sánchez-Sánchez 11:50 Short talk Short talk 6: OmicSHIELD: privacy-protected federated omic data analysis in multi-center studies with Bioconductor through DataSHIELD. Juan Ramon Gonzalez 12:00 Short talk Short talk 7: DepInfeR - A Bioconductor package for Inferring tumor-specific cancer dependencies through integrating ex-vivo drug response assays and drug-protein profiling. Junyan Lu
EuroBioC2022 Live Stream Day 1: morning
Visualization and analysis of highly multiplexed imaging data - Nils Eling
Visualization Analysis IMC Data - March 28, 2022
Spatial Transcriptomics Technologies and Analysis Tools - Dario Righelli Analysing Spatially Resolved Transcriptomics Data with Bioconductor - Helena L. Crowell
Spatial Transcriptomics - January 31, 2022
Rにおけるバイオ画像解析入門: Introduction to Bioimaging Analysis in R 久米 慧嗣 Satoshi Kume (大阪電気通信大学 Osaka Electro-Communication University, 日本 Japan) 4:00 PM - 5:00 PM JST (Japan Standard Time) on Thursday, Nov. 4th, 2021 JAPANESE WORKSHOP このワークショップでは、BioconductorパッケージであるEBImageを使って、Rでの画像処理・画像解析の基本的な方法を扱う。次に、BioImageDbsパッケージを用いて、ExperimentHubからの画像データの取得を行う。さらに、rMiWパッケージが提供する、Deep learningモデルの１つであるU-NETモデルを用いて、教師有り画像セグメンテーション（領域分割）を学び。このワークショップは、Orchestra環境にて実施する。 This workshop covers basic methods of the image processing and image analysis in R using the Bioconductor package “EBImage” and the Orchestra platform. In addition, the image dataset is obtained from ExperimentHub using the “BioImageDbs” package. Using this dataset, we perform a supervised image segmentation using the U-NET model, one of deep learning models, provided by the rMiW package. Moderator: 露崎 弘毅 Koki Tsuyuzaki (理化学研究所 RIKEN, 日本 Japan)
Rにおけるバイオ画像解析入門: Introduction to Bioimaging Analysis in R
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