22938 results for "ega"

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• Human brain development single cell sequencing additional samples

  69 tissue samples from various parts of the developing human embryo brain were dissociated and single cells were collected and processed without bias for mRNA-seq using 10X chromium 3' protocol. Libraries were sequenced on Illumina NovaSeq and reads aligned against the human GRCh38 genome. This is an addition to EGAD00001006049 Human development single cell sequencing, consisting of samples added after the original submission to EGA, but included in final paper.

  Dataset EGAD50000001295

• Haplotype Reference Consortium Release 1.1

  Haplotype Reference Consortium Release 1.1 - subset for release via the EGA

  Dataset EGAD00001002729

• Out with the Java, in with the Python - new EGA data download client unveiled

  We will shortly be deprecating the Java-based download client also known as API V2. The Java client began its life at the back end of 2014, and during its time has seen many developments that have served our users well. During its tenure, the Java client enabled distribution of over 6.5 million files totalling nearly 15 petabytes of data to researchers around the globe. Recent increases in genomic and phenotypic data file sizes, the number of datasets archived in the EGA, the number of users downloading data, and the diversity of download locations has meant that at times the Java client struggled to distribute data efficiently. In response, our team of developers have built a new download client with more robust features and better functionality and reliability. Enter stage left our shiny new API V3.1! The new API V3.1 will replace both API V2 and API V3. The download client for the new API V3.1 is written in Python, and the code is openly available on Github. This Python client makes https calls to the EGA AAI (https://ega.ebi.ac.uk:8443/) and to the EGA Data API (https://ega.ebi.ac.uk:8052), both of which must be accessible from the client location. In addition to general updates to improve performance, the API V3.1 has three new features enhancing the EGA distributions services. First, requested data are now downloaded over secure https connections rather than http, meaning that data can be delivered unencrypted. Instead of separately requesting, downloading, and decrypting data using the Java client, data can now be requested and downloaded using a single command without the need for decrypting. The API V3.1 also automatically verifies each file’s unencrypted md5 after download to ensure the file has downloaded correctly. Second, the new API supports segmenting and automatic resuming. To enable quicker download speeds, the API breaks files into up to four segments and downloads them in parallel. With the new resume feature, downloads - both segmented and continuous stream - will automatically resume if they encounter any errors or the connection is interrupted. These features result in both a faster and more reliable download experience. Finally, the new API V3.1 implements the GA4GH-compliant htsget protocol for supporting requests over genomic ranges. This exciting new feature means that for data files with accompanying index files (e.g. .crai for CRAM files) users can download specific regions of interest rather than the entire file saving both time and storage space. The new features of the Python-based API V3.1 represent significant improvements in security, speed, reliability, and flexibility that are sure to provide a better data download experience. To take full advantage of these features, users must update to Python 3.X. Considering the changes in the data structures with the new API, the upgrade to a new version of the Python client is also mandatory. Updating the client to the latest version can be achieved by running the following command: pip3 install pyega3 -U We are excited for users to try out the new features and take advantage of the multifariously growing EGA distribution services for human biomedical omics data. If you have any questions or feedback, please email the EGA Helpdesk team. We'd love to hear from you!

  Blog new-ega-data-download-client

• Synthetic modeling reveals HOXB genes are critical for the initiation and maintenance of human leukemia

  Study EGAS00001003627

• Evaluation of protocols for rRNA depletion-based RNA sequencing of nanogram inputs of mammalian total RNA

  Study EGAS00001003849

• DAC - Comparison of sequencing assays for sensitive detection of circulating tumour DNA in stage IA-IV breast cancer

  Dac EGAC00001002549

• Exome Resequencing of Progressive Hearing Loss

  Exome resequencing of progressive hearing loss.

  Study EGAS00001000001

• Data Access Committee for data from EGAS00001002864: Genome analysis of oesophageal cancer and Barretts oesophagus

  Dac EGAC00001000863

• 1000IBD Data Access Committee UMCG

  Dac EGAC00001000791

• Molecular Oncology Group, PICR

  Dac EGAC00001000095

• This DAC is to control access to data contained within dataset EGAS00001001147, for Myeloma XI clinical trial patients.

  Dac EGAC00001000307

• Centre for Genomic Regulation - Beta Cell Genome Regulation Lab

  Dac EGAC00001000853

• DAC for present-day Central Asia genotype data at the Centre for GeoGenetics, Natural History Museum of Denmark.

  Dac EGAC00001000894

• DAC for "The application of RNA sequencing for the diagnosis and genomic classification of pediatric acute lymphoblastic leukemia"

  Dac EGAC00001001501

• Detection of ctDNA in Plasma of Patients with Clinically Localised Prostate Cancer is Associated with Rapid Disease Progression

  Dac EGAC00001001718

• BCRC-ICGS (Bladder Cancer Research Centre, Institute of Cancer and Genomic Sciences, Univ. of Birmingham) Data Access Committee

  Dac EGAC00001001982

• Division of Molecular Oncology, National Cancer Center Research Institute Data Access Committee

  Dac EGAC00001002007

• RNA-sequencing of tumors from 45 patients with recurrent or metastatic gastric cancer treated with immune checkpoint inhibitors

  Dac EGAC00001002295

• Whole-exome sequencing of 47 microsatellites stable Early-onset sporadic rectal cancer (EOSRC) tumors and corresponding normal samples.

  Dac EGAC00001002502

• DAC for Clonal somatic copy number altered driver events inform drug sensitivity in high-grade serous ovarian cancer

  Dac EGAC00001002644

• EGAD00000000046

  RNA-SEQ data from 3 recurrent and 1 ovarian primary Granulosa Cell Tumour samples

  Dataset EGAD00000000046

• EGAD00000000047

  Signal data for from 3 recurrent and 1 ovarian primary Granulosa Cell Tumour samples

  Dataset EGAD00000000047

• EGAD00010000662

  Finnish population cohort genotyping

  Dataset EGAD00010000662

• EGAD00010000787

  Epigen-Brasil samples using HumanOmni2.5

  Dataset EGAD00010000787

• EGAD00010000377

  DNA methylation analysis of 6 primary lymphoma samples

  Dataset EGAD00010000377

• EGAD00010000379

  DNA methylation analysis of 2 peripheral blood samples

  Dataset EGAD00010000379

• EGAD00010000570

  Imputation-based meta-analysis of severe malaria in Kenya.

  Dataset EGAD00010000570

• Osteosarcoma Sequencing

  Osteosarcoma Sequencing

  Dataset EGAD00001000007

• Kaposi sarcoma exome

  Kaposi sarcoma exome

  Dataset EGAD00001000071

• MDSMPN Rearrangement Screen

  MDSMPN Rearrangement Screen

  Dataset EGAD00001000073

• Chondrosarcoma Exome

  Chondrosarcoma Exome

  Dataset EGAD00001000125

• Osteosarcoma Whole Genome

  Osteosarcoma Whole Genome

  Dataset EGAD00001000147

• OICR PANCREATIC CANCER DATASET

  OICR PANCREATIC CANCER DATASET

  Dataset EGAD00001000262

• Pulldown cytosine deaminases

  Pulldown cytosine deaminases

  Dataset EGAD00001000245

• Conventional whole genome bisulfite sequencing protocol

  Dataset EGAD00001000601

• Landscape of gene mutations in Down syndrome-related myeloid disorders

  Dataset EGAD00001000628

• MCL bam dataset

  Complete set of bam files associated with study EGAS00001000622

  Dataset EGAD00001000702

• W115 Deep Sequencing

  Dataset EGAD00001000779

• MPNST

  These are only the whole exome sequences

  Dataset EGAD00001001031

• Whole-Genome Bisulfite Sequencing of a paired initial and recurrent glioma

  Dataset EGAD00001001616

• DATA FILES FOR PCGP SJACT WGS

  Dataset EGAD00001001874

• CPCG-BRCA-ARRAY

  Raw Array data from the CPCGene BRCA study

  Dataset EGAD00010001196

• SNP_dataset_1

  Tissue samples using Illumina HumanOmniExpress-FFPE-12 v1.0 BeadChip

  Dataset EGAD00010001179

• papuan-U-1

  Papuan Genotyping

  Dataset EGAD00010001326

• REL-2017-07-1273

  HipSci - Monogenic Diabetes - Genotyping Array - July 2017

  Dataset EGAD00010001334

• REL-2017-07-2005

  HipSci - Hereditary Cerebellar Ataxias - Genotyping Array - July 2017

  Dataset EGAD00010001344

• REL-2017-07-2006

  HipSci - Hereditary Spastic Paraplegia - Genotyping Array - July 2017

  Dataset EGAD00010001346

• REL-2017-07-2012

  HipSci - Primary Immune Deficiency - Genotyping Array - July 2017

  Dataset EGAD00010001358

• UK BioBank Imputed dataset 2018

  UK BioBank Imputed Dataset

  Dataset EGAD00010001474

• ARGO-Larissa GWAS

  The ARGO-Larissa GWAS.

  Dataset EGAD00010000883