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Combining the original replicates and pseudo-replicates for differential binding analysis?
replicates R diffbind chip-seq written 7 days ago by maisarasora • 10
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172
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1
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Is it possible to run DESeq with only two replicates in one group?
replicates deseq2 rna-seq written 9 weeks ago by DataFanatic • 240 • updated 9 weeks ago by ATpoint ♦ 36k
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The number of biological replicates and technical replicates in proteomics experiments
proteomics replicates written 12 weeks ago by wangdp123 • 240 • updated 12 weeks ago by JC ♦ 11k
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How to estimate the inter sample and inter replicate correlation coefficient?
replicates correlation coefficients rna-seq r2 written 3 months ago by DataFanatic • 240
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209
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Forum: DEG analysis when not replicates are available
replicates forum noiseq rna-seq edger written 3 months ago by Antonio R. Franco • 4.5k
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IDR (Irreproducible Discover Rate) on more than two replicates
replicates chip-seq idr peak-calling written 5 months ago by olechnwin • 30 • updated 4 months ago by zhuobaowen • 10
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What is the possibility of replicates being different from other replicates of same sample?
replicates microarray mean error written 5 months ago by Karma • 280
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704
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5 follow
1
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Handling replicates in Chip-seq
replicates chip-seq written 13 months ago by chaudharyc61 • 30 • updated 7 months ago by Biostar ♦♦ 20
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6 follow
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Different number of peaks between biological replicates?
replicates chip-seq sequencing written 9 months ago by rohitsatyam102 • 170 • updated 9 months ago by colin.kern • 920
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Which one to use for ChipSeq replicate comparison: Spearman or Pearson
replicates chip-seq correlation genome written 9 months ago by rohitsatyam102 • 170 • updated 9 months ago by colin.kern • 920
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Advice on Handling Batch Effect in ChIP-seq Experiment
replicates sequencing chip-seq batch effect batch written 11 months ago by dmj6ab • 10
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4.8k
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6 follow
1
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Large Variation In Rpkm Values Of Different Biological Replicates From Cufflinks
replicates rpkm cufflinks deseq written 6.5 years ago by hoangtv • 30 • updated 12 months ago by Biostar ♦♦ 20
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Single Cell RNA Sequencing - replicates pooling and barcoding
scrna-seq barcode replicates pooling written 12 months ago by Bolesaem • 10
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Check for variation between two replicates in transcriptome data
replicates statistical test rna-seq written 12 months ago by sagardesai91 • 50
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411
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macs14 replicates treatment and final wiggle peak files
replicates chip-seq macs14 wig-file written 15 months ago by kashiff007 • 130 • updated 15 months ago by geek_y ♦ 11k
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Bootstrapping a phylogenetic tree using FastTree
replicates bootstrapping phylogenetics fasttree written 17 months ago by ginohino • 0
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Merge MNase-seq bam files from replicates.
replicates mnase-seq merge next-gen bam-files written 17 months ago by kashiff007 • 130
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5 follow
1
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Analysis Without Replicates
replicates without rna-seq written 20 months ago by stevenmarkgalway • 10
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SRA Database: Samples with Multiple Sequencing Runs Per Sample
replicates sra technical replicates written 21 months ago by vlrieg • 10
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DESeq2 for differential expression analysis of RNA-seq datawith few samples per condition?
replicates samples deseq2 rna-seq written 4.8 years ago by amyfm • 10 • updated 23 months ago by Biostar ♦♦ 20
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9 follow
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Replicates for RNA-seq from 1 cell line undergoing different treatments
replicates cell lines rna-seq written 2.6 years ago by azayob • 0 • updated 2.2 years ago by BIOTECH.DEEPTI911 • 10
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10 follow
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How to filter for samples that show good concordance across replicates in DESEQ2 count data from RNA-SEQ?
replicates R deseq2 rna-seq prepde.py written 2.2 years ago by nancy • 80 • updated 2.2 years ago by i.sudbery ♦ 8.4k
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How to deal with (combine) technical replicates (FPKM vs Read count data) for RNA-Seq experiments?
replicates gene expression read count rna-seq written 2.4 years ago by Ameya Kulkarni • 0 • updated 2.4 years ago by Devon Ryan ♦ 96k
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9 follow
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Why Cannot Limma Package Do Differential Expression Between Two Samples Without Replication?
replicates differential-expression limma affymetrix written 7.2 years ago by shangzhong0619 • 20 • updated 2.6 years ago by Biostar ♦♦ 20
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12 follow
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Rna-Seq Biological Replicates...
replicates gene next-gen rna sequencing written 10.2 years ago by Gregory Miles • 100 • updated 2.6 years ago by pshubhamoy • 20
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Calling peaks with macs2 if not all replicates have a corresponding input-file
replicates macs2 chip-seq written 3.3 years ago by jklopp • 0 • updated 3.1 years ago by Biostar ♦♦ 20
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5 follow
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Chips-Seq Replicates And Motif Discovery: What Is The Most Sound Way To Deal With The Merged Peaks (Peak Consensus) ?
replicates chip-seq motif written 6.7 years ago by Nick • 270 • updated 3.7 years ago by Biostar ♦♦ 20
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The Purpose Of The Repeat Experiments
replicates snp genotyping written 9.0 years ago by Zhshqzyc • 490 • updated 4.0 years ago by Biostar ♦♦ 20
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High in group variability RNA seq
replicates variability rna seq written 4.2 years ago by Biogeek • 400
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8
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TMM normalization for RNA seq data with three replicates (2 samples)
replicates edger rna-seq tmm written 4.6 years ago by IrK • 50
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