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<prev • 25 results • page 1 of 1 • next >
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DESeq2 design and batch effect
deseq2 salmon rna-seq batch effect written 2 days ago by georgewwp • 0 • updated 1 day ago by Kevin Blighe • 3.4k
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2
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132
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2
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error when run tximport for salmon files
quantification r error txtimport salmon rna-seq written 10 days ago by Lila M • 370
2
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1
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118
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which option is better for DESeq2 analysis: salmon or htseq-count?
htseq-count de salmon rna-seq written 11 days ago by Lila M • 370 • updated 11 days ago by kristoffer.vittingseerup • 300
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Any suggestions upon re-quantifying bam files downloaded from EBI-EGA archive with Salmon?
bedtools salmon samtools rna-seq written 4 weeks ago by vchris_ngs • 4.0k
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143
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Salmon never completes, stuck on processing fragments
fastq salmon rna-seq written 6 weeks ago by jjrin • 10
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1
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189
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1
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Salmon libType is required but missing, although I thought I supplied it
salmon rna-seq written 3 months ago by charlesmagnefr • 10
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1
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261
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SALMON's warning library type
salmon rna-seq written 4 months ago by biks.kestro • 10 • updated 4 months ago by WouterDeCoster ♦ 22k
3
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1
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253
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1
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salmon, kallisto psuedoaligners are failing to process
aligners salmon kallisto rna-seq written 4 months ago by dr.prasad.bvls • 10 • updated 4 months ago by Rob ♦ 2.1k
3
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2
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2
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Using Ensembl ID History Converter on GRCh37 Transcripts for salmon
ensembl grch37 salmon rna-seq written 5 months ago by stefanos.bamopoulos • 30 • updated 5 months ago by Magali_Ensembl • 130
2
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File containing a mapping of transcripts to genes - Salmon on Galaxy
galaxy salmon rna-seq written 5 months ago by MANISH RANJAN • 40 • updated 5 months ago by Devon Ryan ♦ 71k
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Reference Transcriptome for hg19
salmon transcriptome reference rna-seq hg19 written 6 months ago by stefanos.bamopoulos • 30
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Recommendations for miRNA-Seq quantification with Salmon
transcript quantification salmon mirna-seq written 7 months ago by labadorf • 10
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Common Cutoff in TPM unit to filter out gene considered as low expressed.
tpm salmon rna-seq written 8 months ago by ZheFrench • 60 • updated 8 months ago by Devon Ryan ♦ 71k
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Main difference between RSEM and k-mer based quantification methods
salmon rna-seq rsem kallisto written 8 months ago by uki_al • 20
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342
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1
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Dependencies auto-installed with Conda?
salmon conda nesoni written 10 months ago by Liflock • 0 • updated 8 months ago by Devon Ryan ♦ 71k
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How do you normalize Transcript per Million TPM to compare between samples ?
tpm quantification salmon star rna-seq written 9 months ago by ZheFrench • 60
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342
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featureCounts with pseudobam
featurecounts salmon rna-seq pseudobam kallisto written 9 months ago by mccormack • 20 • updated 9 months ago by genomax ♦ 34k
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417
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What is the Sleuth intercept and how can Sleuth be used when you have >2 treatment types?
sleuth salmon kallisto rna-seq dte written 9 months ago by james.lloyd • 70
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2
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Salmon libtype - Does it matter?
alignment salmon written 14 months ago by Matthias • 10
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Salmon: Optimal k-mer size (for indexing) for RNA-seq data alignment using reference genome
k-mer indexing alignment salmon rna-seq written 15 months ago by BCArg • 40
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909
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Meta analysis of RNA-seq data
salmon meta-analysis rna-seq written 23 months ago by bharata1803 • 230 • updated 21 months ago by Biostar ♦♦ 20
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Salmon warning detected suspicious pair
salmon rna-seq written 23 months ago by bharata1803 • 230 • updated 23 months ago by andrew.j.skelton73 • 3.9k
51
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29 follow
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Current state-of-the-art for RNA-Seq gene / transcript expression quantification OR just the tools of preference
bitseq cufflinks salmon kallisto rna-seq written 2.1 years ago by IV • 1.1k
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Blog: Salmon Kallisto HtSeq-count for gene level analysis - Anecdotal evidence
salmon htseq-count blog kallisto rna-seq written 2.4 years ago by Ido Tamir ♦ 4.8k
87
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47 follow
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Transcript to gene level count for DEseq(2) use- Salmon/Sailfish/Kallisto etc.
rnaseq deseq2 salmon deseq kallisto written 2.4 years ago by mhockin • 450 • updated 2.4 years ago by Michael Love • 1.5k
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