Workflows

cutadapt+BWA-MEM-mis1-i2,2-gapex2,2+filter... (1)

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This workflow is designed to genotype trinucleotide repeats from sequencing reads that span the repeat and its flanksDetailed description as follows:1. Input fastq sequencing reads files (Galaxy tool: Input dataset)Input files for the workflow are single-end MiSeq reads (R1 produced using the protocol from Ciosi et al. 2018) or PacBio reads of insert (ROI) in fastq files format.2. Removing Illumina sequencing adaptor sequence in 3’ of the MiSeq reads (Galaxy tool: Cutadapt 1.16)Cutadapt...

Created: 2020-06-01 | Last updated: 2020-06-01

deneme (1)

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Created: 2020-04-27

Credits: mevlüt Aydemir BAIBU

Deriving factual information from WHO COVI... (1)

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 WHO has posted a CSV that's frequently updated with COVID abstracts. A simple PubMed search reveals thousands of abstracts too. So here's an NLP pipeline to mine these and extract meaningful sentences/facts using Stanford Open Information Extractor and Biological entity tagging. #knime #naturallanguageprocessing #textanalytics #textmining #covid19 #nlp #datascience #WHO 

Created: 2020-04-12

Credits: Insilicoconsulting

Antiviral activity multiclass Predictor (1)

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A simple multi-class antiviral activity predictor based on expanded Pubchem fingerprints and random forest algorithm. Seems to work well to perform quick screens for antiviral molecules.Download training data from CTD (http://ctdbase.org/downloads/) or  use this preprocessed version https://www.myexperiment.org/files/2285.html. Write to me at rajeev.gangal@gmail.com regarding any queries.I make no claim that the predictive model is accurate for clinical hypotheses or that it will find mo...

Created: 2020-03-23 | Last updated: 2020-03-25

Credits: Insilicoconsulting

Phosphoproteomics of short-term Hedgehog s... (1)

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HPLC-MS/MS proteomics Analysis of human medulloblastoma cell line (DAOY cell line)15 minutes treatment with SAG, vismodegib, EGFTMT 10 plex experiment20 pH8 fractions measured using Qexactive HFKnime Workflow

Created: 2019-08-22 | Last updated: 2019-08-23

Credits: Tamara Scheidt

Phosphoproteomics of short-term Hedgehog s... (1)

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HPLC-MS/MS proteomics Analysis of human medulloblastoma cell line (DAOY cell line)5 minutes treatment with SAG, vismodegib, EGFTMT 10 plex experiment20 pH8 fractions measured using Qexactive HFKnime Workflow

Created: 2019-08-22 | Last updated: 2019-08-23

Credits: Tamara Scheidt

Phosphoproteomics of short-term Hedgehog s... (1)

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HPLC-MS/MS phosphoproteomics Analysis of human medulloblastoma cell line (DAOY cell line)15 minutes treatment with SAG, vismodegib, EGFTMT 10 plex experiment13 HILIC fractions measured using Qexactive HFKnime Workflow

Created: 2019-08-22 | Last updated: 2019-08-23

Credits: Tamara Scheidt

Phosphoproteomics of short-term Hedgehog s... (1)

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HPLC-MS/MS phosphoproteomics Analysis of human medulloblastoma cell line (DAOY cell line)5 minutes treatment with SAG, vismodegib, EGFTMT 10 plex experiment12 HILIC fractions measured using Qexactive HFKnime Workflow

Created: 2019-08-22 | Last updated: 2019-08-23

Credits: Tamara Scheidt

Untargeted metabolomics reveals molecular ... (1)

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Normal 0 false false false EN-US X-NONE AR-SA ...

Created: 2019-06-21

Credits: David_MTX

Integrative data mining of chemical compou... (1)

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This workflow downloads ligand data for hepatic Organic Anion Transporting Polypeptides (OATPs) from five different open sources (CHEMBL, Metrabase, USFC-FDA Transportal, IUPHAR, and Drugbank) in an semi-automatized fashion. This workflow can be adopted to any other ligand data showing an (in)activity against membrane transporter. If missing, structural file format is mapped via PubChem webservices. Pre-curated compounds are subjected to standardization procedure (Atkinson standardization scr...

Created: 2018-12-10 | Last updated: 2018-12-10

Credits: Alzbeta Tuerkova