Tag: GSA

Preprint peer review gains momentum with new

4 December 2023 – Review Commons, a platform dedicated to the peer review of preprints, announces the expansion of its family of affiliate journals to include publications from three additional organizations. Affiliate journals accept the transfer of peer-reviewed preprints directly from the Review Commons online portal into their editorial workflow, where they are assessed…

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Browse – GSA – CNCB-NGDC

Browse – GSA – CNCB-NGDC      Home GSA SRA1757663 SRA1757663 Information Title: SUB14000603 Release date: 2023-11-26 Data Source: NCBI Center Name:The John Paul II Catholic University of Lublin Lab Name:Faculty of Medicine Read more…

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Sol-Gel Technologies Ltd to Host Virtual KOL Event on Gorlin Syndrome and the Upcoming Phase 3 Trial for SGT-610 – Sol-Gel Technologies (NASDAQ:SLGL)

Event to be held on December 6, 2023 will focus on preventing basal cell carcinomas associated with Gorlin syndrome with a discussion of the disease burden, SGT-610 and the upcoming Phase 3 trial NESS ZIONA, Israel, Nov. 28, 2023 (GLOBE NEWSWIRE) — Sol-Gel Technologies, Ltd. SLGL (“Sol-Gel”), a dermatology company…

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Sol-Gel Technologies Ltd to Host Virtual KOL Event on Gorlin Syndrome and the Upcoming Phase 3 Trial for SGT-610

Sol-Gel Technologies Ltd. Event to be held on December 6, 2023 will focus on preventing basal cell carcinomas associated with Gorlin syndrome with a discussion of the disease burden, SGT-610 and the upcoming Phase 3 trial NESS ZIONA, Israel, Nov. 28, 2023 (GLOBE NEWSWIRE) — Sol-Gel Technologies, Ltd. (Nasdaq: SLGL)…

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Sol-Gel Technologies Ltd to Host Virtual KOL Event on

Event to be held on December 6, 2023 will focus on preventing basal cell carcinomas associated with Gorlin syndrome with a discussion of the disease burden, SGT-610 and the upcoming Phase 3 trial NESS ZIONA, Israel, Nov. 28, 2023 (GLOBE NEWSWIRE) — Sol-Gel Technologies, Ltd. (Nasdaq: SLGL) (“Sol-Gel”), a dermatology…

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Gedmatch MDLP K16 Oracle Results Bolivian Family : 23andme

Rules General Be Civil. Racist, sexist and or hateful comments/posts are absolutely not tolerated here. Treat fellow Redditors with respect. No targeted harassment of any kind. Any violation of this rule will end with a warning or ban, depending on the severity of the violation. Punishment is ultimately down to…

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Could a new CRISPR gene editing technology lead to innovation in aquaculture?

22 November 2023 Responsible Seafood Advocate Innovative CRISPR gene editing technology tailored for aquaculture improves safety and unimpeded legal accessibility The CRISPR-Cas3 platform provides unique advantages, such as increased safety through a reduction in unintended mutations and the capability for broad gene alterations near the target site. Photo: Eggs Microinjection…

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Let’s see some mtdna L haplogroup, what’s yours , I am L3f1b : 23andme

Rules General Be Civil. Racist, sexist and or hateful comments/posts are absolutely not tolerated here. Treat fellow Redditors with respect. No targeted harassment of any kind. Any violation of this rule will end with a warning or ban, depending on the severity of the violation. Punishment is ultimately down to…

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Early detection of hepatocellular carcinoma via no end-repair enzymatic methylation sequencing of cell-free DNA and pre-trained neural network | Genome Medicine

Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F. Global cancer statistics 2020: GLOBOCAN estimates of incidence and mortality worldwide for 36 cancers in 185 countries. CA Cancer J Clin. 2021;71(3):209–49. Article  PubMed  Google Scholar  Llovet JM, Kelley RK, Villanueva A, Singal AG, Pikarsky E,…

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DNA doesn’t lie but do the companies when they present the results?

Hi, Martin. A very recent, er, few words in this G2G topic about comparison differences among the testing and reporting companies, and a bit about the processes and algorithms underlying them. Not only will you get varying centimorgan estimations, but the companies that show you segment detail will very, very seldom be in agreement even…

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Do different microarray chips yield different accuracy of polygenic scores?

When replicating a polygenic score, labs have multiple microarray chips to choose from. (E.g., GSA, GDA, UK Biobank Axiom Array, UK BiLEVE Axiom array, GeneChip 2.0 array, Infinium Core-24 Kit, etc.). Will using different chips impact the accuracy of the polygenic score? If so, by how much? I’ve been unable…

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University of Manitoba Events Calendar

University of Manitoba Events Calendar – R for Data Visualization (ggplot2) …

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mc3so MSCVLR CAMEL Support subscription Option when CAMEL phase 3 is not

USER MANUAL <osmsso> Originating SMS CAMEL denied Subscription Option (0-2), Application system dependent parameter. <tsmsso>Terminating SMS CAMEL phase 4 denied subscription option(0-2), Application system dependent parameter. <mmso> Mobility Management CAMEL denied Subscription Option (0-2), Application system dependent parameter. <mty>Match Type, possible values are “E”(Enabling) or “I” (Inhibiting). <dnum>Destination Number expressed…

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Generation of UL128-shRNA transduced fibroblasts for the release of cell-free virus from clinical human cytomegalovirus isolates

Human cytomegalovirus (HCMV) is a herpesvirus that is widespread in the population worldwide [1,2], where it remains latent after infection in its host for a lifetime [3–5]. While primary infection or reactivation in immunocompetent individuals usually remains subclinical and causes little or no symptoms, it can cause severe damage in…

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Genotyping, sequencing and analysis of 140,000 adults from Mexico City

Recruitment of study participants The MCPS was established in the late 1990s following discussions between Mexican scientists at the National Autonomous University of Mexico (UNAM) and British scientists at the University of Oxford about how best to measure the changing health effects of tobacco in Mexico. These discussions evolved into…

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Quality Control of VCFs that used different genotyping arrays

I have three VCFs. Two of these VCFs were generated using the Precision Medicine Research Array (PMRA) and refer to SNPs as AX numbers. I was able to merge the two PMRA VCFs together. Merged PMRA VCFs (Total genotyping rate is 0.924427): 1 AX-150343089 0 837711 T C 1 AX-149471710…

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QC of genetic data

QC of genetic data 0 Hi, I have some genetic data in a bim file. The chromosomes range from 0 to 23 and 26, which I have not come across before. Would the SNPs on chromosome 0 and 26 be removed from the genetic file or left in. Then, I…

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Idat raw data conversion

Idat raw data conversion 0 Hello everybody We have just started genotyping with GSA and generated first idat files. To QC we were advices to use GenomeStudio and for that we downloaded all the necessary files: bpm, egt, imap files from illumina website. Yet when we performed analysis in Genomestudio,…

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what is the mean of the file “*._f1.fq.gz” and “*._r2.fa.gz”

what is the mean of the file “*._f1.fq.gz” and “*._r2.fa.gz” 1 Hello, I downloaded the files from: bigd.big.ac.cn/gsa/ The file is ended with: ” *._f1.fq.gz” and ” *._r2.fa.gz”. Is it single-end or paired-end sequencing? If it is paired-end sequencing, the file should be: ” *._r1.fq.gz” and ” *._r2.fa.gz”, not ”…

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10X scRNA-seq v2 odd fastq format

10X scRNA-seq v2 odd fastq format 1 Hi Biostars, I’ve downloaded some scRNA-Seq data from the GSA, which I am hoping to analyze. This is 10x V2 chemistry sequence data. However the format is different from what I am familiar with. First, the reads come in 2 fastq files (“f1”…

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Detecting drug resistance of Mycobacterium tuberculosis

Introduction According to the World Health Organization report 2022, the incidence rate of tuberculosis in China is 7.4%, with a year-on-year increase of 1.6%. China ranks third globally in terms of tuberculosis cases, with the top three countries being developing nations.1 It is worth noting that the tuberculosis mortality rate…

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Effect of a microencapsulated probiotic on the intestinal microbiome of Pacific white shrimp

21 August 2023 Chung-Hung Liu Microencapsulation of Bacillus subtilis E20 proved effective in addressing probiotic issues related to inclusion during feed manufacturing Results of this study showed that microencapsulation was effective in addressing probiotic issues related to inclusion during feed manufacturing, that encapsulated B. subtilis E20 administration increased beneficial strains…

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A diverse ancestrally-matched reference panel increases genotype imputation accuracy in a underrepresented population

In the present study, we enrolled 412 participants from the Southeast Asian Brugada syndrome cohort (ClinicalTrials.gov number, NCT04232787). The study was approved by the Institutional Review Board (IRB) of the Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand (IRB No. 431/58). All methods were performed in accordance with relevant guidelines/regulations. Informed…

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Enrichment analysis on scRNSseq on which genes/clusters perform ReactomeGSA and GSEA?

Enrichment analysis on scRNSseq on which genes/clusters perform ReactomeGSA and GSEA? 0 Hi all, I have a question about gene ontology/GSEA and reactome analyses on scRNAseq dataset. I don’t understand on which genes/clusters is correct to perform these analyses? Do I have to perform these analysis on all clusters (post…

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Creating a teleost fish traceability program based on genetic data from the Pacific coast of Panama

24 July 2023 Carlos Ramos-Delgado, Ph.D. A total of 34 species from 14 families were identified at the species level from 164 sequences This research provides important information and molecular tools for accurate identification of marine fish species in Panama and their traceability along the supply chain by providing species-specific…

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Productions Manager job with UNIVERSITY OF SURREY

GSA Location: Guildford Salary: £35,308 to £43,155 Post Type: Full Time Closing Date: 23.59 hours BST on Sunday 13 August 2023 Reference: 032423 Guildford School of Acting at the University of Surrey is one of the most highly regarded conservatoires in the UK, with a vibrant community of performers, performance makers,…

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Global DNA and Gene Chip Market to Reach USD 14.03 Billion by 2028, Fueled by Wide Application in Diverse Sectors

Reports And Data The Global DNA and Gene Chip Market is projected to grow at a CAGR of 11.4% from USD 5.84 Billion in 2020 to USD 14.03 Billion in 2028. NEW YORK CITY, NY, UNITED STATES, June 21, 2023/EINPresswire.com/ — The global DNA and Gene Chip Market is expected…

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glm sample size vs OBS_CT

I am running glm with plink2. See code below: PLINK v2.00a3.6 AVX2 (14 Aug 2022)             www.cog-genomics.org/plink/2.0/(C) 2005-2022 Shaun Purcell, Christopher Chang   GNU General Public License v3Logging to /PROJECTES/HELIX_OMICS/analyses/GWAS_chemical_exposure_ZB/results/phthalates_mb/mecpp/mecpp.log.Options in effect:  –bfile /PROJECTES/HELIX_OMICS/data_final/gwas/child/8y/GSA_QC3.HRCimp_20210615/HELIX.impQC.rs.05.EUR  –covar /PROJECTES/HELIX_OMICS/analyses/GWAS_chemical_exposure_ZB/db/HELIX_phtalates_cov_plink.txt  –covar-name PC1, PC2, PC3, PC4, PC5, PC6, PC7, PC8,…

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protein abrupt-like isoform x1, maker-scaffold97_size377342-snap-gene-2.14 (gene) Tigriopus kingsejongensis

Associated RNAi Experiments Homology BLAST of protein abrupt-like isoform x1 vs. L. salmonis genes Match: EMLSAG00000011120 (supercontig:LSalAtl2s:LSalAtl2s753:207020:208693:1 gene:EMLSAG00000011120 transcript:EMLSAT00000011120 description:”augustus_masked-LSalAtl2s753-processed-gene-1.1″) HSP 1 Score: 342.043 bits (876), Expect = 1.286e-109Identity = 269/559 (48.12%), Postives = 311/559 (55.64%), Query Frame = 0 Query: 168 DNFGPSAPKRHRFNGPESRNSPSSSPKSLADWGRRSLEPKTEDTAEADNNNSTPKSESLLSQALEKHSNVSSMYDRHLLRDNGDGRDGDSASDTTSERPESLMDGLIKNSGAESELHRQLSAASPASMGGHLFPPGLEALYRQAGFPSAFLGLAAGAA—-GGSPGG————–PVSSMHGLASSVPQVGLQSHAGNPN—————————————–LAGKLDMMRVRATDPRPCPKCGKIYRSAHTLRTHMEDKHTICPGYRCVLCGTVAKSRNSLHSHMSRQHRGISTKDLPVLPMPSPFDPALASRLLAKAGVKVTPNELAARASPTAPRRSDLPKLDTNLLHM-HHHQFPLPPSLPT-SMSGHMGRGSHDGNGSDVEDLRVSSAPSPFGSNGGPGGIYSQAHQMRIAQGMLSPKDFA–ALASAGGAQGAAGMGSALLDTYLSMI-AAAGGDSNPMAAALNFQ-NPASRAAAFAAAAAAASGNQAHNGDGKDNDQRSGVSEDRDDMTGELGSDADNDDLSDNDD 661 D++ P PKRHR NG E…

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Interferon-gamma is quintessential for NOS2 and COX2 expression in ER- breast tumors that lead to poor outcome

Cell culture The MDA-MB231 (MB231) human breast cancer cell line was obtained from the American Type Culture Collection (ATCC, Manassas, VA) and grown in RPM1-1640 (Invitrogen) supplemented with 10% fetal bovine serum (FBS; Invitrogen, Waltham, MA) at 37 °C in a humidified atmosphere of 5% CO2 in the air. Cells were…

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Promising Scholars Recognized with McCrone Awards | Humboldt NOW

Cal Poly Humboldt professors Oscar Vargas, Biological Sciences; Paul Michael Leonardo Atienza, Critical Race, Gender & Sexuality Studies (CRGS); and Rouhollah Aghasaleh, School of Education, are recipients of the 2023 McCrone Promising Faculty Scholars Award. Selected for exhibiting potential in a specific field, each faculty member will receive $1,500 to…

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How much can I rely on DNA segments less than 8CM

Part 2 A brief summary of the data is at this Google Sheet. I’ve been (casually, not earnestly) thinking about trying to locate a child and both parents who have done a 30X WGS or better, and at least a couple of their cousins (preferably 2nd through 4th) who also have…

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Aerial transport of bacteria by dust plumes in the Eastern Mediterranean revealed by complementary rRNA/rRNA-gene sequencing

Katra, I. et al. Richness and diversity in dust stormborne biomes at the Southeast Mediterranean. Sci. Rep. 4, 5265 (2014). Article  CAS  Google Scholar  Kellogg, C. A. & Griffin, D. W. Aerobiology and the global transport of desert dust. Trends Ecol. Evolution 21, 638–644 (2006). Article  Google Scholar  Mazar, Y.,…

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R: PC gamma

PCgamma {GSAgm} R Documentation PC gamma Description For GSA of SNP data, the following two-step procedure is implemented (see Biernacka et al[1] for more details on the method). Step 1: Principal components analysis for SNPs within a gene is completed with the components needed to explain 80 percent of the…

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GSA – Galaxy Community Hub

Galaxy-GSA – Galaxy Community Hub ← Platform Directory comments Gene Set Analysis (GSA) can be defined as the comparison of a query gene set (a list or a rank of differentially expressed genes, for example) to a reference database of annotated gene sets, in order to interpret the initial query…

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17q12-21 risk-variants influence cord blood immune regulation and multitrigger-wheeze

Background: Childhood wheeze represents a first symptom of asthma. Early identification of children at risk for wheeze related to 17q12-21 variants and their underlying immunological mechanisms remain unknown. We aimed to assess the influence of 17q12-21 variants and mRNA-expression at birth on development of wheeze. Methods: Children were classified as…

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I can’t get a dossage file using PLINK

Hi, I have been trying to get a dosage file from vcf, map and fam files. For that, I have written this bash script : plink –fam plink.fam –map plink.map –dosage one.vcf –write-dosage However, I got this error: –dosage: Reading from one.vcf. Error: Line 1 of one.vcf has fewer tokens…

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Phasing with SHAPEIT

Edit June 7, 2020: The code below is for pre-phasing with SHAPEIT2. For phased imputation using the output of SHAPEIT2 and ultimate production of phased VCFs, see my answer here: A: ERROR: You must specify a valid interval for imputation using the -int argument, So, the steps are usually: pre-phasing…

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Single cell DNA sequencing reveals punctuated and gradual clonal evolution in hepatocellular carcinoma

Footnotes Grant support This work is jointly supported by National Natural Science Foundation of China (82173035, 81802813,82030079, 81972656, 81988101, and 81902401), the National Science and Technology Major Project of China (2018ZX10723204), the Michigan Medicine and Peking University Health Science Center Joint Institute for Translational and Clinical Research (BMU2020JI005), Natural Science…

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working with .gmt files

working with .gmt files 3 Hi! I have downloaded a pathway data set in .gmt format form the GSEA website. I’m wondering how can I properly read this data set in R. Could anyone help me? Thank you!   myposts • 9.5k views • link updated 2 hours ago by…

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