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198 Research products, page 1 of 20

  • Research software
  • Other research products
  • 2013-2022
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  • Research software . 2022
    Open Access
    Authors: 
    William T Clarke; Jack J Miller;
    Publisher: Zenodo
    Project: WT | Wellcome Centre for Integ... (203139)

    Spec2nii is a program for multi-format conversion of in vivo MRS to the NIfTI-MRS format. Spec2nii is developed at the Wellcome Centre for Integrative Neuroimaging (FMRIB), at the University of Oxford. It is hosted at github.com/wtclarke/spec2nii.

  • Open Access
    Authors: 
    Combrisson, Etienne; Basanisi, Ruggero; Cordeiro, Vinicius Lima; Ince, Robin A.A; Brovelli, Andrea;
    Publisher: Zenodo
    Project: WT | Beyond Pairwise Connectiv... (214120)

    New Features frites.conn.conn_links now accepts to use brain region names as source or target seeds (8d7e1fb6) New function frites.stats.confidence_interval for computing confidence intervals, standard deviation (sd) and standard error on the mean (sem) on numpy arrays and xarray DataArray (3a512537) New plotting module with two functions for plotting connectivity matrices, frites.plot.plot_conn_heatmap and frites.plot.plot_conn_circle (7a107d100e, a480371a74, 33930cc33a1, 24029c4cf6b) Add the possibility to control the node's size in frites.plot.plot_conn_circle (7454376b) Add support for signed connectivity and improve node control of frites.plot.plot_conn_circle (78bbb91c) Bug fixes Fix parallel computing of frites.conn.conn_covgc (f2ff5f67) Use linearly spaced indices instead of closest time points in frites.conn.define_windows (b5443ac2) frites.conn.conn_spec average over tapers after computing connectivity metric (10966a1be3).Thanks to @adam2392 and @ruuskas from the mne-connectivity package.

  • Open Access English
    Authors: 
    Muffato, Matthieu; Surana, Priyanka;
    Publisher: Zenodo
    Project: WT | Darwin Tree of Life (218328)

    The pipeline takes a CSV file that contains assembly accession number, Ensembl species names (as they may differ from Tree of Life ones !), output directories, and geneset versions. Assembly accession numbers are optional. If missing, the pipeline assumes it can be retrieved from files named ACCESSION in the standard location on disk. The pipeline downloads the Fasta files of the genes (cdna, cds, and protein sequences) as well as the GFF3 file. All files are compressed with bgzip, and indexed with samtools faidx or tabix. 📜Steps involved: Download from Ensembl the GFF3 file, and the sequences of the genes in Fasta format. Compress and index all Fasta files with bgzip, samtools faidx, and samtools dict. Compress and index the GFF3 file with bgzip and tabix. 🛠 Fixed since v1.0.0 When a samplesheet is provided, do not process the individual command-line parameters 🔗 All dependencies are automatically fetched by Singularity. bgzip samtools tabix python3 wget cut gzip nextflow 22.04.0 or later singularity or docker

  • Open Access English
    Authors: 
    Muffato, Matthieu; Surana, Priyanka;
    Publisher: Zenodo
    Project: WT | Darwin Tree of Life (218328)

    The pipeline takes a CSV file that contains assembly accession number, Ensembl species names (as they may differ from Tree of Life ones !), output directories. Assembly accession numbers are optional too. If missing, the pipeline assumes it can be retrieved from files named ACCESSION in the standard location on disk. The pipeline downloads the repeat annotation as the masked Fasta file and a BED file. All files are compressed with bgzip, and indexed with samtools faidx or tabix. 📜Steps involved: Download the masked fasta file from Ensembl. Extract the coordinates of the masked regions into a BED file. Compress and index the BED file with bgzip and tabix. 🔗 All dependencies are automatically fetched by Singularity. bgzip samtools tabix python3 wget cut gzip nextflow 22.04.0 or later singularity or docker

  • Open Access
    Authors: 
    Nardus Mollentze; Deborah Keen; Uuriintuya Munkhbayar; Roman Biek; Daniel G. Streicker;
    Publisher: Zenodo
    Project: WT | Mitigating bat viruses: f... (217221), UKRI | Viral Genomics and Bioinf... (MC_UU_12014/12)

    Code and data used in Mollentze et al. (2022), Variation in the ACE2 receptor has limited utility for SARS-CoV-2 host prediction. Preprint. New in this version: Additional tests and figures added in response to peer review (https://www.biorxiv.org/content/10.1101/2022.05.16.492068v1#review). Full changelog: https://github.com/nardus/ace2/compare/v1.0.0...v1.1.0

  • Open Access English
    Authors: 
    Lucinde, Ruth Khadembu; Abdi, Abdirahman; Orindi, Benedict; Mwakio, Stella; Gathuri, Henry; Onyango, Edwin; Chira, Salome; Ogero, Morris; Isaaka, Lynda; Shangala, Jimmy; +32 more
    Publisher: Zenodo
    Project: WT | Core Support for the East... (203077)

    These files contain the SPIRIT checklist and study flow diagram for the SONIA Trial. This trial is a pragmatic randomized controlled trial of standard care versus steroids plus standard care for treatment of pneumonia in adults admitted to Kenyan hospitals.

  • Open Access English
    Authors: 
    Muffato, Matthieu; Surana, Priyanka;
    Publisher: Zenodo
    Project: WT | Darwin Tree of Life (218328)

    The pipeline takes an assembly Fasta file (possibly compressed), runs fasta_windows on it, and transforms the outputs into files more practical for downstream use. 📜 Steps involved: Run fasta_windows on the assembly Fasta file. Extract single-statistics bedGraph files from the multi-statistics TSV files fasta_windows outputs. Compress and index all bedGraph and TSV files with bgzip and tabix. 🔗 All dependencies are automatically fetched by Singularity. fasta_windows bgzip tabix python3 cut gzip nextflow 22.04.0 or later singularity or docker

  • Open Access English
    Authors: 
    Muffato, Matthieu; Surana, Priyanka;
    Publisher: Zenodo
    Project: WT | Darwin Tree of Life (218328)

    The pipeline takes a CSV file that contains assembly accession number, Ensembl species names (as they may differ from Tree of Life ones !), output directories, and geneset versions. Assembly accession numbers are optional. If missing, the pipeline assumes it can be retrieved from files named ACCESSION in the standard location on disk. The pipeline downloads the Fasta files of the genes (cdna, cds, and protein sequences) as well as the GFF3 file. All files are compressed with bgzip, and indexed with samtools faidx or tabix. 📜Steps involved: Download from Ensembl the GFF3 file, and the sequences of the genes in Fasta format. Compress and index all Fasta files with bgzip, samtools faidx, and samtools dict. Compress and index the GFF3 file with bgzip and tabix. 🔗 All dependencies are automatically fetched by Singularity. bgzip samtools tabix python3 wget cut gzip nextflow 22.04.0 or later singularity or docker

  • Open Access English
    Authors: 
    Muffato, Matthieu; Surana, Priyanka;
    Publisher: Zenodo
    Project: WT | Darwin Tree of Life (218328)

    The pipeline takes an assembly accession number, as well as the assembly name, and downloads it. It also builds a set of common indices (such as samtools faidx), and extracts the repeat-masking performed by the NCBI. 📜 Steps involved: Download from the NCBI the genomic sequence (Fasta) and the assembly stats and reports files. Turn the masked Fasta file into an unmasked one. Compress and index all Fasta files with bgzip, samtools faidx, and samtools dict. Generate the .sizes file usually required for conversion of data files to UCSC's "big" formats, e.g. bigBed. Extract the coordinates of the masked regions into a BED file. Compress and index the BED file with bgzip and tabix. 🛠 Fixed since v1.0.0 BED files were not tabix-indexed with the right settings Fasta files now have the .fa extension, rather than .fasta 🎀 Added since v1.0.0 New species_dir column to indicate where to download the files to 🔗 All dependencies are automatically fetched by Singularity. bgzip samtools tabix python3 wget awk gzip nextflow 22.04.0 or later singularity or docker

  • Research software . 2022
    Open Access
    Authors: 
    William T Clarke; Jack J Miller;
    Publisher: Zenodo
    Project: WT | Wellcome Centre for Integ... (203139)

    Spec2nii is a program for multi-format conversion of in vivo MRS to the NIfTI-MRS format. Spec2nii is developed at the Wellcome Centre for Integrative Neuroimaging (FMRIB), at the University of Oxford. It is hosted at github.com/wtclarke/spec2nii.

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