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16 materials found

Keywords: Structures  or Flow cytometry data 


EMBL-EBI Train Online

If you work in the life sciences, you may find that you’re spending less time doing experiments and more time analysing huge amounts of biological data. Train online is here to help you do this quickly and efficiently.

Scientific topics: Bioinformatics

Keywords: Bioinformatics, Chemical biology, Cross domain, Dna rna, Gene expression, Literature, Ontologies, Proteins, Structures, Systems

EMBL-EBI Train Online https://tess.elixir-europe.org/materials/embl-ebi-train-online If you work in the life sciences, you may find that you’re spending less time doing experiments and more time analysing huge amounts of biological data. Train online is here to help you do this quickly and efficiently. Bioinformatics Bioinformatics, Chemical biology, Cross domain, Dna rna, Gene expression, Literature, Ontologies, Proteins, Structures, Systems Beginner informatics Life sciences 2018-05-11
PDBe: Searching for biological macromolecular structures

PDBe: Searching for biological macromolecular structures from http://www.ebi.ac.uk/training/online/course/pdbe-searching-biological-macromolecular-structure.

Keywords: Proteins, Chemical biology, Structures

PDBe: Searching for biological macromolecular structures https://tess.elixir-europe.org/materials/pdbe-searching-for-biological-macromolecular-structures PDBe: Searching for biological macromolecular structures from http://www.ebi.ac.uk/training/online/course/pdbe-searching-biological-macromolecular-structure. Proteins, Chemical biology, Structures 2016-05-26
Flow Cytometry 2013 Module 4 - 1D Static gating

How to create a constant gate for the whole data set for one channel by first creating a sample representative of the whole data set How to apply a static gate to all samples and count the proportions of cells lying on either side of the gate Visualizing the proportions using a density...

Keywords: 1d static gating, Flow cytometry data

Flow Cytometry 2013 Module 4 - 1D Static gating https://tess.elixir-europe.org/materials/flow-cytometry-2013-module-4-1d-static-gating How to create a constant gate for the whole data set for one channel by first creating a sample representative of the whole data set How to apply a static gate to all samples and count the proportions of cells lying on either side of the gate Visualizing the proportions using a density plot, histogram, bean/violin plot Automating a sequential gating strategy in R to obtain cell proportions for a desired phenotype 1d static gating, Flow cytometry data 2013-06-26 2017-10-09
Flow Cytometry 2013 Module 6 - Clustering and Additional FCM Tools

Lecture on FlowCAP (Flow Cytometry: Critical Assessment of Population Identification Methods) project K-means explained flowMeans: smart k-means for FCM data flowClust3.0, SPADE, flowBin, flowFP, SamSPECTRAL clustering Biomarker discovery: flowType and RchyOptimyx, advanced tools used...

Keywords: Biomarker discovery, Flow cytometry data, Flowcap

Flow Cytometry 2013 Module 6 - Clustering and Additional FCM Tools https://tess.elixir-europe.org/materials/flow-cytometry-2013-module-6-clustering-and-additional-fcm-tools Lecture on FlowCAP (Flow Cytometry: Critical Assessment of Population Identification Methods) project K-means explained flowMeans: smart k-means for FCM data flowClust3.0, SPADE, flowBin, flowFP, SamSPECTRAL clustering Biomarker discovery: flowType and RchyOptimyx, advanced tools used to explore novel phenotypes and find ones which correlate with a clinical diagnosis More R: Bioconductor.org, an open source software project full of bioinformatics packages created for R, including sample work flows GenePattern.org: web-interface for running analysis modules such as sample deidentication, extracting specic keywords, quality control, normalization, clustering, classification FlowRepository.org: online FCM data repository to share public or private data sets with collaborators while providing detailed descriptions of the experiment set up and each FCS file Biomarker discovery, Flow cytometry data, Flowcap 2013-06-26 2017-10-09
Flow Cytometry 2013 Module 5 - 1D Dynamic gating

Using quantiles to set a gate based on a negative control Using median and standard deviation to set a gate based on a negative control Exploring rangeGate: an automated way to set a 1D gate for each sample individually Recording proportions of cells in subpopulations of interest by...

Keywords: 1d dynamic gating, Flow cytometry data

Flow Cytometry 2013 Module 5 - 1D Dynamic gating https://tess.elixir-europe.org/materials/flow-cytometry-2013-module-5-1d-dynamic-gating Using quantiles to set a gate based on a negative control Using median and standard deviation to set a gate based on a negative control Exploring rangeGate: an automated way to set a 1D gate for each sample individually Recording proportions of cells in subpopulations of interest by creating a spreadsheet file Recording a visual record of the gating results by creating JPEG image files 1d dynamic gating, Flow cytometry data 2013-06-26 2017-10-09
Flow Cytometry 2013 Module 3 - Preprocessing and Quality Assurance of FCM Data

Preprocessing Removing margin events Data transformation: log vs. biexponential Data normalization Quality Assurance Overview of quality assurance concepts: total raw/viable cell count, margin event count, outlier detection based on density of common...

Keywords: Flow cytometry data, Preprocessing, Quality assurance

Flow Cytometry 2013 Module 3 - Preprocessing and Quality Assurance of FCM Data https://tess.elixir-europe.org/materials/flow-cytometry-2013-module-3-preprocessing-and-quality-assurance-of-fcm-data Preprocessing Removing margin events Data transformation: log vs. biexponential Data normalization Quality Assurance Overview of quality assurance concepts: total raw/viable cell count, margin event count, outlier detection based on density of common parameters Building quality assurance objects using flowQ and generating summary HTML reports Flow cytometry data, Preprocessing, Quality assurance 2013-06-26 2017-10-09
PDBePISA: Identifying and interpreting the likely biological assemblies of a protein structure

PDBePISA: Identifying and interpreting the likely biological assemblies of a protein structure from http://www.ebi.ac.uk/training/online/course/pdbepisa-identifying-and-interpreting-likely-biolo, added automatically.

Keywords: Proteins, Structures

PDBePISA: Identifying and interpreting the likely biological assemblies of a protein structure https://tess.elixir-europe.org/materials/pdbepisa-identifying-and-interpreting-the-likely-biological-assemblies-of-a-protein-structure PDBePISA: Identifying and interpreting the likely biological assemblies of a protein structure from http://www.ebi.ac.uk/training/online/course/pdbepisa-identifying-and-interpreting-likely-biolo, added automatically. Proteins, Structures 2016-03-05
PDBeFold: Searching for structural homologues of a protein

PDBeFold: Searching for structural homologues of a protein from http://www.ebi.ac.uk/training/online/course/pdbefold-searching-structural-homologues-protein, added automatically.

Keywords: Proteins, Structures

PDBeFold: Searching for structural homologues of a protein https://tess.elixir-europe.org/materials/pdbefold-searching-for-structural-homologues-of-a-protein PDBeFold: Searching for structural homologues of a protein from http://www.ebi.ac.uk/training/online/course/pdbefold-searching-structural-homologues-protein, added automatically. Proteins, Structures 2016-03-05
PDBeChem: Searching for small molecules and small molecule fragments

PDBeChem: Searching for small molecules and small molecule fragments from http://www.ebi.ac.uk/training/online/course/pdbechem-searching-small-molecules-and-small-molec.

Scientific topics: Small molecules

Keywords: Proteins, Chemical biology, Structures

PDBeChem: Searching for small molecules and small molecule fragments https://tess.elixir-europe.org/materials/pdbechem-searching-for-small-molecules-and-small-molecule-fragments PDBeChem: Searching for small molecules and small molecule fragments from http://www.ebi.ac.uk/training/online/course/pdbechem-searching-small-molecules-and-small-molec. Small molecules Proteins, Chemical biology, Structures 2016-04-22
PDBe: Searching the Protein Data Bank

PDBe: Searching the Protein Data Bank from http://www.ebi.ac.uk/training/online/course/pdbe-searching-protein-data-bank.

Keywords: Proteins, Chemical biology, Structures

PDBe: Searching the Protein Data Bank https://tess.elixir-europe.org/materials/pdbe-searching-the-protein-data-bank PDBe: Searching the Protein Data Bank from http://www.ebi.ac.uk/training/online/course/pdbe-searching-protein-data-bank. Proteins, Chemical biology, Structures 2016-05-26
PDBe: Quick tour

PDBe: Quick tour from http://www.ebi.ac.uk/training/online/course/pdbe-quick-tour.

Keywords: Proteins, Structures

PDBe: Quick tour https://tess.elixir-europe.org/materials/pdbe-quick-tour PDBe: Quick tour from http://www.ebi.ac.uk/training/online/course/pdbe-quick-tour. Proteins, Structures 2016-05-26
PDBe: Exploring a Protein Data Bank (PDB) entry

PDBe: Exploring a Protein Data Bank (PDB) entry from http://www.ebi.ac.uk/training/online/course/pdbe-exploring-protein-data-bank-pdb-entry.

Keywords: Proteins, Chemical biology, Structures

PDBe: Exploring a Protein Data Bank (PDB) entry https://tess.elixir-europe.org/materials/pdbe-exploring-a-protein-data-bank-pdb-entry PDBe: Exploring a Protein Data Bank (PDB) entry from http://www.ebi.ac.uk/training/online/course/pdbe-exploring-protein-data-bank-pdb-entry. Proteins, Chemical biology, Structures 2016-06-14
PDBe: An introduction to search and entry pages: webinar

PDBe: An introduction to search and entry pages: webinar from http://www.ebi.ac.uk/training/online/course/pdbe-introduction-search-and-entry-pages-webinar.

Keywords: Proteins, Chemical biology, Structures

PDBe: An introduction to search and entry pages: webinar https://tess.elixir-europe.org/materials/pdbe-an-introduction-to-search-and-entry-pages-webinar PDBe: An introduction to search and entry pages: webinar from http://www.ebi.ac.uk/training/online/course/pdbe-introduction-search-and-entry-pages-webinar. Proteins, Chemical biology, Structures 2016-04-14
Complex Portal: webinar

Complex Portal: webinar from http://www.ebi.ac.uk/training/online/course/complex-portal-webinar.

Keywords: Systems, Ontologies, Proteins, Structures

Complex Portal: webinar https://tess.elixir-europe.org/materials/complex-portal-webinar Complex Portal: webinar from http://www.ebi.ac.uk/training/online/course/complex-portal-webinar. Systems, Ontologies, Proteins, Structures 2016-06-14
Complex Portal: Quick tour

Complex Portal: Quick tour from http://www.ebi.ac.uk/training/online/course/complex-portal-quick-tour.

Keywords: Systems, Ontologies, Proteins, Structures

Complex Portal: Quick tour https://tess.elixir-europe.org/materials/complex-portal-quick-tour Complex Portal: Quick tour from http://www.ebi.ac.uk/training/online/course/complex-portal-quick-tour. Systems, Ontologies, Proteins, Structures 2016-06-14
ChEMBL: Exploring bioactive drug-like molecules

ChEMBL: Exploring bioactive drug-like molecules from http://www.ebi.ac.uk/training/online/course/chembl-exploring-bioactive-drug-molecules.

Keywords: Chemical biology, Structures

ChEMBL: Exploring bioactive drug-like molecules https://tess.elixir-europe.org/materials/chembl-exploring-bioactive-drug-like-molecules ChEMBL: Exploring bioactive drug-like molecules from http://www.ebi.ac.uk/training/online/course/chembl-exploring-bioactive-drug-molecules. Chemical biology, Structures 2016-06-14