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hisat2-stringtie-ballgown pipeline gives high p-value and q-value for RNA-seq of Arabidopsis thaliana
ballgown arabidopsis stringtie rna-seq hisat2 written 19 months ago by tiancaigg • 10 • updated 6 days ago by 20482485 • 0
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TAIR Gene Symbols
arabidopsis genetics genomics written 25 days ago by pthom010 • 0 • updated 25 days ago by genomax ♦ 91k
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Gene set enrichment (GSEA) - Arabidopsis - Public RNA-seq data
arabidopsis rna-seq gsea written 10 weeks ago by sumanth • 0 • updated 10 weeks ago by ashish • 540
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Biomart query returns NA when searching for entrez_id, while manual search works
R biomart arabidopsis refseq written 4 months ago by eggrandio • 40 • updated 4 months ago by Kevin Blighe ♦ 66k
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8 follow
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TFBS enrichiment analysis
gene R jaspar arabidopsis tfbstools written 21 months ago by mannoulag1 • 60 • updated 7 months ago by Alex Reynolds ♦ 31k
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Arabidopsis thaliana RNA-Seq analysis: Is 68% transcript annotation acceptable/expected with Ensembl ref and new tuxedo pipeline
new tuxedo ensembl stringtie arabidopsis rna-seq written 10 months ago by arctic • 20
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Arabidopsis Gene ID Conversion (BioMart, CLC Genomics Workbench Output)
R biomart arabidopsis rna-seq written 17 months ago by jamesfischer047 • 10 • updated 10 months ago by Biostar ♦♦ 20
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Dealing with spike-in reads that overlap between two genomes
drosophila spike-in arabidopsis chip-seq written 14 months ago by juanpjlozano • 0 • updated 14 months ago by colin.kern • 930
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GATK best practice step-by-step command lines for Arabidopsis DNA-Seq data analysis
gatk dna-seq arabidopsis written 18 months ago by wangdp123 • 250 • updated 18 months ago by Pierre Lindenbaum ♦ 131k
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Trying to get 1001 population Arabidopsis genotype and SNPs data
R 1001_genomes arabidopsis gwas farmcpu written 20 months ago by ycth8 • 0
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Gene not found in Affymetrix expression profiles
geo arabidopsis thaliana affymetrix written 24 months ago by lorenzo_fabbri • 10 • updated 24 months ago by h.mon ♦ 31k
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GWAS or QTL mapping for arabidopsis quantitative traits?
qtl gwas arabidopsis written 24 months ago by joshsteiner5 • 0
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Create a cytoband file for arabidopsis thanilana TAIR10 data. RCircos plot
bed cytoband rcircos arabidopsis written 2.5 years ago by dzisis1986 • 20
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SNP/indel annotation in Arabidopsis
indel varscan arabidopsis snp written 2.5 years ago by Federico Giorgi • 630 • updated 2.5 years ago by finswimmer ♦ 13k
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photosynthesis genes of the plant 'arabidopsis'
R photosynthesis arabidopsis kegg microarray written 3.4 years ago by mannoulag1 • 60 • updated 3.4 years ago by theobroma22 • 1.1k
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Using Plant GO Slim in topGO
plant go slim gene ontology topgo arabidopsis written 3.5 years ago by Sreeraj Thamban • 170
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miR KEGG enrichment in Arabidopsis
enrichment arabidopsis mir kegg mirna written 3.6 years ago by jnf3769 • 40
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5 follow
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Quick and Dirty Gene Network
arabidopsis network interactions gene network written 3.6 years ago by jnf3769 • 40 • updated 3.6 years ago by vakul.mohanty • 240
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Download the Entire Set of Raw Transcriptome data for Arabidopsis thaliana
transcriptome trinity arabidopsis rna-seq assembly written 4.4 years ago by ruwangikagunawardana • 10 • updated 4.4 years ago by rlapoint11 • 30
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Arabidopsis GFF files
gff arabidopsis written 5.9 years ago by biolab • 1.2k • updated 4.4 years ago by Biostar ♦♦ 20
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Explanation of how to efficiently use the TAIR database for finding homologs of cDNA? BLAST, FASTA, Wu-BLAST
genome fasta cdna arabidopsis ests written 4.5 years ago by zak4.0 • 0 • updated 4.5 years ago by Denise CS • 5.1k
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Where to batch download Arabidopsis gene expression data?
arabidopsis expression written 5.1 years ago by biolab • 1.2k • updated 5.1 years ago by zoo741 • 70
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Cufflinks for Arabidopsis.. Ensembl or TAIR 10
cufflinks tair10 arabidopsis ensembl written 5.4 years ago by mfahim • 10 • updated 5.4 years ago by Antonio R. Franco • 4.5k
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Alternative spliced genes in A. thaliana
arabidopsis rna-seq alternatesplicing exonskipping written 5.9 years ago by kandoigaurav • 150
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viewing BED Graph files on the IGB
bedgraph arabidopsis igb written 5.9 years ago by akivab2 • 100 • updated 5.9 years ago by Ann • 2.3k
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Detected Variants' Effect on Primary Structure of a Protein (Arabidopsis)
genome arabidopsis snp written 6.1 years ago by shanika.amarasinghe • 30 • updated 6.0 years ago by Emily_Ensembl ♦ 21k
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How to find a FASTA (CDS) of specified sequence?
gene fasta sequence glutamine synthase arabidopsis written 6.5 years ago by JorgeGonzalez • 20 • updated 6.5 years ago by mikhail.shugay ♦ 3.4k
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CuffLinks predicts too long UTR for overlapping genes
cufflinks tair10 arabidopsis rna-seq written 6.5 years ago by Ann • 2.3k • updated 6.5 years ago by Istvan Albert ♦♦ 85k
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