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Kallisto/Sleuth - issue when using own annotations in the sleuth_prep() function
R sleuth kallisto rna-seq written 2 days ago by BioBing • 70
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1
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137
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1
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GSEA produces too few enriched sets
kallisto gsea transcriptome written 3 days ago by crimsontabaq • 30 • updated 3 days ago by kristoffer.vittingseerup • 80
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2
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653
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2
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ENSEMBL Transcript_Accession ID conversion
ensembl sleuth kallisto rna-seq written 15 months ago by dinindu.senanayake • 0 • updated 11 days ago by WouterDeCoster ♦ 18k
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1
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101
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salmon, kallisto psuedoaligners are failing to process
aligners salmon kallisto rna-seq written 18 days ago by dr.prasad.bvls • 10 • updated 18 days ago by Rob ♦ 1.8k
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109
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Subset of transcripts - Do I need to re-scale the TPM values?
tpm kallisto rna-seq written 22 days ago by user230613 • 240
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107
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Getting average fragment length for single end reads
differential expresion kallisto rna-seq written 4 weeks ago by Sreeraj Thamban • 30 • updated 4 weeks ago by Buffo • 460
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181
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kallisto: strand-specific and fragment length calculation
kallisto rna-seq written 5 weeks ago by user230613 • 240 • updated 5 weeks ago by pmelsted • 50
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3
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183
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Help for finding the right FASTA file for kallisto
fasta kallisto rna-seq written 6 weeks ago by swamyvinny • 0 • updated 6 weeks ago by Sreeraj Thamban • 30
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137
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transcript to gene mapping after sleuth run
R sleuth biomart rna-seq kallisto written 7 weeks ago by bioinfo8 • 60
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203
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Will variance between the number of reads mapped in samples impact my differential analysis?
sleuth kallisto rna-seq written 7 weeks ago by a.rex • 60 • updated 7 weeks ago by Istvan Albert ♦♦ 71k
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127
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sequencing QC metrics from kallisto
kallisto written 11 weeks ago by alerodriguez • 30
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1
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214
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1
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RNASeq reads from two bacterial species
trinity co-culture kallisto rsem rna-seq written 3 months ago by alyamahmoud • 0 • updated 3 months ago by h.mon ♦ 6.6k
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490
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Using kallisto for metagenomic analysis
metagenomics kallisto written 8 months ago by igor • 4.3k
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251
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Main difference between RSEM and k-mer based quantification methods
salmon rna-seq rsem kallisto written 4 months ago by uki_al • 20
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316
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Understanding Sleuth output for multiple samples
sleuth kallisto rna-seq written 4 months ago by Bharat Iyengar • 230
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245
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featureCounts with pseudobam
featurecounts salmon rna-seq pseudobam kallisto written 5 months ago by mccormack • 20 • updated 5 months ago by genomax ♦ 29k
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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 5 months ago by james.lloyd • 70
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233
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kallisto to metaseqR
R next-gen kallisto rna-seq written 6 months ago by bioinfo8 • 60
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Sleuth: Combined lrt and wt tests, clustered heatmap
R sleuth kallisto rna-seq heatmap written 6 months ago by bioinfo8 • 60
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Is Sleuth a good package?
R sleuth kallisto rna-seq written 8 months ago by student-t • 380 • updated 8 months ago by Devon Ryan ♦ 68k
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418
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RNA-Seq without replicate using Kallisto
kallisto rna-seq written 8 months ago by weixiaokuan • 70
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511
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finding significance between transcripts in a RNA-Seq experiment
tximport deseq2 limma edger kallisto written 10 months ago by Assa Yeroslaviz • 1.1k
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346
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Malloc_error_break and job termination while running Kallisto
kallisto rna-seq memory written 11 months ago by MagnumOpus • 0
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2
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425
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Significance within conditions
dexseq deseq2 cuffdiff kallisto rna-seq written 11 months ago by Assa Yeroslaviz • 1.1k
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differential gene expression using sleuth
sleuth kallisto rna-seq written 15 months ago by frida.danielsson • 10 • updated 14 months ago by cpcantalapiedra • 130
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Using 'tximport' library for downstream DGE after quantifying with Kallisto
tximport R kallisto rna-seq written 14 months ago by Sinji • 2.4k • updated 14 months ago by Michael Love • 1.4k
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get gene ids running sleuth kallisto for differential gene expression
sleuth kallisto rna-seq written 15 months ago by frida.danielsson • 10
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450
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Reg: Changing outliers in RNASEQ
kallisto rsem rna-seq written 15 months ago by harishk0201 • 10
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Kallisto vs Cufflinks
fpkm cufflinks kallisto rna-seq written 15 months ago by frida.danielsson • 10
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following Kallisto with DESeq2 using tximport package
tximport ensembl deseq2 kallisto ucsc written 17 months ago by Assa Yeroslaviz • 1.1k • updated 16 months ago by Michael Love • 1.4k
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