Showing :Normalization•reset
1
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57
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Normalization for two bulk RNA datasets with different library sizes
NormalizationBulkRNA-seqDESeq2
1 day agoK.• 0• updated 1 day agoMichael Love 31k
0
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1
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64
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错误使用cqn的包
Normalizationcqn
5 weeks agopegah.taklifi• 10• updated 5 weeks agoJames W. MacDonald 55k
2
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2
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91
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Normalisation in DESeq2
DESeq2Normalization
7 weeks ago • updated 6 weeks agoBine• 0
1
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2
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136
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Analyzing publicly available DESeq2 normalized counts for differential expression
DifferentialExpressionDESeq2Normalization
8 weeks agokrovi138• 0• updated 7 weeks agoMichael Love 31k
2
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3
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135
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Normalization for within-sample gene correlation
edgeRNormalizationDESeq2tpmRNASeq
8 weeks agotcalvo• 40• updated 8 weeks agoGordon Smyth 41k
0
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2
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89
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extract certain subpopulation of MouseGastrulationData
MouseGastrulationDataNormalizationBatchEffect
8 weeks agoxyang2• 120• updated 8 weeks agoJonathan Griffiths• 30
0
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3
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453
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Is it possible in DiffBind to specify sizeFactors for DESeq2 analysis?
diffbindnormalization
4.5 years agonfursova.msu• 0• updated 10 weeks agoRory Stark♦ 3.5k
1
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4
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768
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MAnorm output as DiffBind input.
MAnormdiffbindnormalizationchipseq
3.0 years agoajeet• 0• updated 10 weeks agoRory Stark♦ 3.5k
0
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1
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173
Views
Normalisation of protein micro array data using VSN
microarraynormalizationprotein
19 months agokeniajin• 0• updated 10 weeks agoWolfgang Huber 13k
0
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10
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204
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Do I have clustering by library size?
PCADESeq2Normalizationlibrarysize
11 weeks agopkachroo• 10• updated 10 weeks agoMichael Love 31k
1
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8
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232
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Spike-in normalization in EdgeR
CUTandRUNedgeRNormalizationSpikeInChIPSeq
11 weeks ago • updated 10 weeks agoHesh• 0
1
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1
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193
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News:Extensive updates in DiffBind 3.0
NormalizationATACSeqChIPSeqDiffBindchipseq
11 weeks agoRory Stark♦ 3.5k
7
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8
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283
Views
How to get gene length for RPKM directly from DGEList object in latest edgeR?
NormalizationedgeRRPKM
12 weeks agoanikng• 0• updated 12 weeks agoGordon Smyth 41k
1
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5
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134
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DESeq2 Normalization causing overcorrection in libaries sizes for a few samples
deseq2normalization
12 weeks agoasrour• 0• updated 12 weeks agoMichael Love 31k
2
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7
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210
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EdgeR diffSpliceDGE: Obtaining exon-level counts and normalisation step
edgernormalizationdifferential exon usagesplicing
3 months agooakhamwolf• 0• updated 3 months agoYunshun Chen• 690
1
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5
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111
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DESeq2 library composition adjustment in size factors
deseq2normalization
3 months agotwfs• 0• updated 3 months agoMichael Love 31k
1
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5
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94
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technical replicates and normalization/log transformation
deseq2normalization
4 months agoA• 40• updated 4 months agoMichael Love 31k
0
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2
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80
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can negative value microarray matrix data analysed by limma directly
limmamicroarraynormalization
4 months agolinouhao• 0• updated 4 months agoKevin Blighe 2.3k
1
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2
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79
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tcga and geo train and validation sets
deseq2normalization
4 months agolinouhao• 0• updated 4 months agoMichael Love 31k
0
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2
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77
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How to normalise data in ballgown?
rnormalizationedger
4 months agolakshmi9c• 0• updated 4 months agoJames W. MacDonald 55k
2
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4
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108
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Deseq2's geometric mean calculation and 0s
deseq2normalization
4 months agolmrogers34• 0• updated 4 months agoMichael Love 31k
6
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13
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343
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How to use RSEM value to find differentially expressed genes
RSEMlimmaedgeRvoomnormalization
4 months agoharelarik• 50• updated 4 months agoGordon Smyth 41k
2
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3
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102
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Differential gene expression using Ballgown
rnormalization
4 months agolakshmi9c• 0
1
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2
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71
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Unexpected rlog values when count spread is large
deseq2normalization
5 months agoeric.blanc• 0• updated 5 months agoMichael Love 31k
2
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8
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235
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Differential gene expression using R
deseq2edgernormalizationlimma
5 months agolakshmi9c• 0• updated 5 months agoGordon Smyth 41k
2
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4
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477
Views
Deconvolution with CIBERSORT: input data
normalizationrvstcibersort
5 months agoMatan G.• 30• updated 5 months agoKevin Blighe 2.3k
2
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2
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87
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Using EdgeR after importing transcript abundance (by SALMON) with tximport
edgernormalization
5 months agoahmedaalkarim• 0• updated 5 months agoJames W. MacDonald 55k
0
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1
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58
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Input of tscR
microarraynormalizationtscRtime-course
5 months agokeremwai• 0• updated 5 months agoKevin Blighe 2.3k
0
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0
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76
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EDASeq: is it possible to normalize within lanes for more than one covariate?
EDASeqnormalizationGClengthRNASeq
5 months agoabf• 30
0
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2
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82
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ChIP-seq MA plot possibly skewed - how to normalise?
DiffBindMA plotnormalizationChIP-seq
5 months agohasse.bossenbroek• 0• updated 5 months agoRory Stark♦ 3.5k
2
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6
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209
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Question: Method to get normalize allele specific read counts
edgernormalization
6 months agohemantcnaik• 0• updated 6 months agoAaron Lun♦ 26k
0
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0
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38
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According to SCBN method, is it possible to acquire normalized data for virtualziation?
SCBNnormalization
6 months agotofukaj• 0
7
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10
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147
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is there a function in edger the same as vst or rlog in deseq2
edgernormalizationdeseq2
7 months agolinouhao• 0• updated 7 months agoGordon Smyth 41k
2
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1
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128
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Cross-species analysis and normalization with DESeq2
normalizationdeseq2across speciesrnaseq
7 months agormurray2050• 0• updated 7 months agoMichael Love 31k
4
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10
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116
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how to analyze WGCNA results?
cancerprobedeseq2annotationnormalization
8 months agorajpal22288• 10• updated 8 months agoKevin Blighe 2.3k
0
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1
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98
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DESeq2 and Heatmap for multiple conditions
deseq2normalization
8 months agoHamidreza Hashemi• 20• updated 8 months agoMichael Love 31k
2
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7
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126
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ControlGenes/ housekeeping genes Deseq2
normalizationdeseq2sizefactors
8 months agomankadeep2• 20• updated 8 months agoMichael Love 31k
4
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3
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877
Views
How to plot the batch corrected values in DESeq2
deseq2normalization
2.0 years agodhwani.dholakia• 0• updated 8 months agoMichael Love 31k
0
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4
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394
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pheatmap for DEGs
normalizationpheatmap
8 months agoHamidreza Hashemi• 20• updated 8 months agoKevin Blighe 2.3k
0
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2
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133
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DESeq2/EdgeR for differential binding analaysis after RepEnrich2
deseq2edgeRrepenrich2normalization
9 months agomkmwong• 0
0
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3
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53
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Unbalanced design and large difference in number of input reads for DESeq2
deseq2normalization
9 months agojillian.waters• 0• updated 9 months agoMichael Love 31k
0
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2
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53
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Error in DESeqDataSet: variables and colnames don't match when they do
deseq2normalization
9 months agoericmalekos• 0• updated 9 months agoBob Thurman• 0
0
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3
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58
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错误:依赖‘AnnotationDbi’not available for package 'hgu133plus2cdf'
normalization
9 months agoshenjun_renji• 0• updated 9 months agoGordon Smyth 41k
0
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1
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53
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Removing low sequences before analysis
deseq2normalization
9 months agompuli011• 0• updated 9 months agoMichael Love 31k
0
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1
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61
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Length scaled TPM and orthologous genes, from Tximport package
normalization
9 months agocossardg• 0• updated 9 months agoMichael Love 31k
0
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8
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103
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Combining 2 datasets from 2 different RNAseq experiments
deseq2normalizationprobe
9 months agol.s.wijaya• 0• updated 9 months agoMichael Love 31k
0
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4
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81
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Issues with normalizing viral-infected single cell data
scanscatersingle cellnormalization
9 months agoJenny Drnevich♦ 2.0k• updated 9 months agoAaron Lun♦ 26k
0
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3
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88
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DEseq2 design tutorial with multiple experimental factors
deseq2annotationnormalization
9 months agochristophe.vanhaver• 0
2
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1
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54
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Using DESeq2 for normalization of dataset with no replicates
normalizationdeseq2
10 months agoHadi Hosseini• 0• updated 10 months agoMichael Love 31k
0
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0
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31
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DESeq2 analysis with scaled continues variables
normalization
10 months agoDo it!• 0
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Comment: Replace a specific nucleotide sequence, at a specific position, with another inbyKonstantinos Yeles • 40
Hello @Benjamin-24571 for your example, I can suggest you this code: Read <- c("1","2","3","4") Sequences <- c("ACACCCACG", "AA…
Comment: CHIP Seq Analysis by DiffBind Packagebyshrinka.genetics • 0
Hello Thanks for your reply. I changed my file format and now it ran. It gave one plot also. All file s are in same directory. No…
Answer: Installing Bioconductor packages in DockerbyKonstantinos Yeles • 40
Hello, @adklts-21974 My way to do the installation of packages in a docker is like this: FROM bioconductor/bioconductor_docker…
Comment: HTqPCR: dealing with technical replicates (filterCategory) and inability to analbylarissa.stanberry • 0
I ran into the same issue. It appears that filtering does not carry over featureData with the exception of featureNames, e.g. call featureD…
Comment: Design Matrix for DESeq2 or EdgeRbyKevin Blighe 2.3k
Cross-posted on Biostars: https://www.biostars.org/p/484823/
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Comment: Normalization for two bulk RNA datasets with different library sizes
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Replace a specific nucleotide sequence, at a specific position, with another in Biostrings
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