Showing : r • reset
2
votes
27
replies
6.3k
views
CRISPRseek package: be aware that as of Oct 2015, CRISPRseek works best for for regions < 200kb
crisprseek sgrna crispr cas9 R
10.4 years ago • updated 10.3 years ago alexgraehl ▴ 20
3
votes
26
replies
6.3k
views
How to prepare targets.txt file in codelink.
r codelink
updated 10.9 years ago by ▴ 760 • written 10.9 years ago by ▴ 260
2
votes
23
replies
5.4k
views
Coping with a label/class imbalance in DESeq2
deseq2 rnaseq r regression
updated 9.4 years ago by 43k • written 9.4 years ago by • 0
1
vote
22
replies
6.8k
views
problem with makeOrgPackageFromNCBI when making an annotation package
bioconductor R annotationforge
updated 9.2 years ago by ▴ 10 • written 9.6 years ago by • 0
5
votes
22
replies
7.0k
views
sqliteSendQuery error in AnnotationForge bioconductor package
bioconductor annotationforge annotationdbi annotation r
updated 9.6 years ago by ★ 1.1k • written 11.0 years ago by • 0
0
votes
19
replies
2.9k
views
Paired Difference Analysis
deseq2 R differential gene expression
8.6 years ago • updated 8.5 years ago nhua • 0
1
vote
19
replies
30k
views
Import bamfiles for RNAsequencing analysis
R rnaseq bam file
updated 7.8 years ago by 53k • written 7.8 years ago by ▴ 10
3
votes
18
replies
3.8k
views
Annotating codelink data file
r codelink annotation annotationdbi
updated 10.8 years ago by ▴ 760 • written 10.8 years ago by ▴ 260
2
votes
18
replies
4.4k
views
Using tximport on rsem files produces error while trying to read in files
R tximport rnaseq tpm rsem
7.9 years ago stephan.emmrich ▴ 10
4
votes
17
replies
4.2k
views
Question about decideTests function and adj.p.value in "limma" R Package
limma r differential gene expression
updated 8.6 years ago by 53k • written 8.6 years ago by ▴ 120
0
votes
17
replies
3.2k
views
How to check linear model
modalmatrix limma R linear
3.0 years ago Jitendra ▴ 10
34
votes
16
replies
50k
views
Differential expression analysis starting from TPM data
R TPM
updated 8.6 years ago by 53k • written 8.6 years ago by ▴ 100
3
votes
16
replies
6.6k
views
How to add pseudocount to DESeq2 dds object
deseq2 r
updated 4.3 years ago by ▴ 10 • written 5.5 years ago by ▴ 10
3
votes
16
replies
5.9k
views
Any way to proceed duplicate removal for list of GRanges object ?
r grangeslist duplicate
updated 9.2 years ago by 25k • written 9.2 years ago by ▴ 80
7
votes
16
replies
5.5k
views
How to extract phastcons score for all protein coding genes and lncRNAs using GenomicScores?
genomicscores granges phastCons100way.UCSC.hg38 r rtracklayer
updated 15 months ago by • 0 • written 6.0 years ago by ▴ 120
3
votes
16
replies
3.7k
views
Atena package - error (new user)
RNAseq R Atena
3.4 years ago • updated 3.1 years ago lalanis1 • 0
22
votes
15
replies
12k
views
biomaRt error unable to fix: need help troubleshooting
biomaRt RNASeqData R
updated 2.3 years ago by ▴ 10 • written 3.9 years ago by ▴ 50
7
votes
15
replies
8.8k
views
Differentially expressed genes selection with FC and FDR cutoff
edgeR rnaseq r bioconductor
updated 7.7 years ago by 53k • written 7.7 years ago by ▴ 60
0
votes
15
replies
3.9k
views
Is the STRINGdb server down?
STRINGdb R protein
updated 6.8 years ago by • 0 • written 6.9 years ago by • 0
5
votes
14
replies
6.4k
views
Connection Refused on port 9000 - RCytoscape
rcytoscape r network graphBAM object
updated 10.2 years ago by ★ 8.2k • written 10.2 years ago by ▴ 50
4
votes
14
replies
10k
views
Extracting custom post-normalization counts from DESeq2
deseq2 r ruvseq normalization rnaseq
10.6 years ago nickp60 • 0
5
votes
14
replies
7.9k
views
Possible ways to select differential expressed genes using DeSeq2 or edgeR
R deseq2 edger differential gene expression fold change
updated 3.8 years ago by ★ 5.0k • written 7.6 years ago by ▴ 60
0
votes
14
replies
4.7k
views
Error in ReactomePA
r reactomepa
updated 9.7 years ago by ★ 1.2k • written 9.7 years ago by ▴ 20
2
votes
14
replies
10k
views
Calculating rpkm from counts data?
r featurecounts rpkm tpm edger
updated 3.0 years ago by ▴ 20 • written 8.6 years ago by ▴ 120
17
votes
14
replies
56k
views
LogFC: how do you determine the cutoff for differentially expressed genes?
rnaseq differential gene expression logfc limma R
updated 3.7 years ago by • 0 • written 8.6 years ago by ▴ 20
0
votes
14
replies
3.4k
views
Path to file in windows
bioconductor R windows diffbind
updated 8.8 years ago by ▴ 670 • written 8.9 years ago by • 0
1
vote
13
replies
3.5k
views
Why Differential expression results differ with edgeR and limma ?
limma edgeR differential gene expression r
8.5 years ago Biologist ▴ 120
0
votes
13
replies
15k
views
KEGG enrichment in R and gene IDs
KEGG enrichKEGG R entrezid
2.9 years ago Laia ▴ 10
2
votes
13
replies
4.5k
views
problems filtering antigenomic probes from HTA 2.0
pd.hta.2.0 R
9.5 years ago • updated 9.0 years ago s.munster ▴ 40
7
votes
13
replies
4.3k
views
Finding the coordinates from a BCV plot in edgeR
r edgeR estimatedispersions coordinate
10.2 years ago pertille • 0
10
votes
13
replies
5.6k
views
Trouble identifying differentially expressed genes on Affymetrix Human Gene 2.0.ST using R with oligo and limma package
R limma oligo differential gene expression affymetrix microarrays
updated 10.7 years ago by • 0 • written 10.7 years ago by ▴ 10
7
votes
13
replies
3.6k
views
Test whether expression levels of two gene sets are significantly different
R DESeq2 gene set testing gene expression
9.3 years ago Jon Bråte ▴ 270
1
vote
12
replies
3.3k
views
How can I integrate set of compressedList in multiple list into one without duplication?
r iranges findoverlaps IntegerList List
9.6 years ago • updated 9.3 years ago jian_liangli • 0
5
votes
12
replies
11k
views
Filtering step for differential analysis in edgeR
r edger differential gene expression filtering bioconductor
updated 7.8 years ago by 53k • written 7.8 years ago by ▴ 120
1
vote
12
replies
4.8k
views
Is there a need or general principle/rule to assess whether the data types/distribution etc is suitable for limma R package to derive differential fe…
limma highthroughputassays R
updated 2.1 years ago by • 0 • written 4.3 years ago by ▴ 380
0
votes
12
replies
2.7k
views
DESeq2 different versions
rnaseq r deseq2
updated 8.3 years ago by 43k • written 8.3 years ago by • 0
1
vote
12
replies
2.1k
views
Taking much longer time for same script after R upgrade to 4.0
R
5.7 years ago hsiowa2 ▴ 20
8
votes
11
replies
15k
views
R: error while reading .h5 files from R using rdhf5 package
rhdf5 r hdf5
updated 2.8 years ago by • 0 • written 8.7 years ago by ▴ 10
0
votes
11
replies
5.1k
views
Remove NaN from a list or replace NaN with a value.
R meta-analysis
updated 4.5 years ago by • 0 • written 7.3 years ago by • 0
6
votes
11
replies
3.0k
views
"associated_gene" attribute from biomaRt returns too few values - SNP(rsID dataset)
r biomart SNP annotation HUGO
updated 5.6 years ago by ★ 6.6k • written 5.6 years ago by • 0
8
votes
11
replies
2.9k
views
Creating design matrix in LIMMA
limma microarray R
9.1 years ago sgblackpearl • 0
5
votes
11
replies
4.8k
views
DESeq2 logfoldchange and interaction in model
deseq2 R logfoldchange rna-seq
6.7 years ago • updated 6.6 years ago pierre.marin • 0
6
votes
11
replies
9.1k
views
How do I split GRange object (set of genomic ranges with 2 metadata column) by chromosome?
granges split r
updated 4.2 years ago by ▴ 40 • written 10.1 years ago by ▴ 80
0
votes
11
replies
3.2k
views
Advice on designing an EdgeR object in complex experimental setup ?
rRDPData r
3.9 years ago • updated 3.8 years ago Mohamed ▴ 30
2
votes
10
replies
3.0k
views
DiffBind consensus peak help
diffbind r chipseq
updated 8.5 years ago by ★ 5.3k • written 8.5 years ago by • 0
5
votes
10
replies
5.8k
views
what should I do with many zero counts from Salmon quantification
Salmon DESeq2 normalization r
updated 7.1 years ago by 43k • written 7.1 years ago by • 0
2
votes
10
replies
2.6k
views
Am I on the right tracks with a 3 factor design in Limma?
r limma design matrix biobase
updated 7.7 years ago by 53k • written 7.7 years ago by • 0
4
votes
10
replies
11k
views
How can I extract sequences from a FASTA file for each of the intervals defined in a BED file using R?
R bioconductor granges
10.1 years ago • updated 9.7 years ago pertille • 0
5
votes
10
replies
3.5k
views
caught segfault error when loading S4Vectors package in R
R S4Vectors segfault
updated 7.0 years ago by 25k • written 7.0 years ago by ▴ 30
2
votes
10
replies
22k
views
Heatmap with error message: `x' must be a numeric matrix
r heatmap numericmatrix
updated 10.0 years ago by ★ 1.5k • written 10.0 years ago by ▴ 120
1,163 results • Page 1 of 24
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Answer: Unable to find ENTREZ IDs by James W. MacDonald 68k
Those are the 'symbols', and are a concatenation of LOC and the NCBI Gene ID (what used to be called an Entrez Gene ID). As an example:http…
Answer: Inconsistencies between accessor functions for TxDb databases with selected seql by a2a2hd42aa • 0
Technical inconsistencies in database accessors can disrupt your workflow, but finding a reliable source to download online mobile games sh…
Comment: Can sample-level weights be used when analysing GSVA scores in limma? by A.Barden ▴ 20
Thanks both for this useful information.
Comment: Reproducibility of code in various Bioconductor versions by Gordon Smyth 53k
SNPlocs.Hsapiens.dbSNP155.GRCh38 is available for download from the same location as always. It has not changed since Bioc 3.20: Presumabl…
Comment: Changing multiple display parameters of a specific exon in GeneRegionTrack by a2a2hd42aa • 0
Similarly, for structural complexity in the [He777 Game][1] APK, having precise control over every detail is what makes a high-performance …
Votes
Do I map probes to gene symbols BEFORE or AFTER differentially expressed gene analysis?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Can sample-level weights be used when analysing GSVA scores in limma?
Comment: Can sample-level weights be used when analysing GSVA scores in limma?
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
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