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How to compare two datasets of proteomic analysis when there are unique and common proteins?
proteomics mass spectrometry protein replication
3.1 years ago by Farah ▴ 80
2
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2
replies
1.6k
views
How to deal with the issue when STRING database could not find a protein, or instead matched its similar protein?
proteomics STRING interaction network uniprot
updated 3.1 years ago by ▴ 70 • written 3.1 years ago by ▴ 80
4
votes
11
replies
1.5k
views
How to write it in R language?
R function programming coding
updated 3.2 years ago by ▴ 140 • written 3.2 years ago by ▴ 80
0
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0
replies
1.1k
views
What is the criteria for defining a CRAPome cut-off score for filtering proteomics datasets?
crapome proteomics filtering cut-off score
3.2 years ago by Farah ▴ 80
0
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0
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529
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What is the number of spectra in a mass spectrometry dataset containing list of proteins?
proteomics Mass spectrometry spectra MS spectra
3.2 years ago by Farah ▴ 80
0
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1
reply
1.1k
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What is the most efficient way of discovering bait-prey interaction networks and mapping biological process relationships within a network?
cytoscape proteomics interaction networks ClueGO
updated 3.3 years ago by ▴ 620 • written 3.3 years ago by ▴ 80
1
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1
reply
2.0k
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Which tool for clustering (sub-networking) of protein-protein interaction networks based on the Gene Ontology Biological Process of proteins?
cytoscape clustering Gene Ontology sub-network
updated 3.4 years ago by ▴ 620 • written 3.4 years ago by ▴ 80
4
votes
4
replies
1.8k
views
Ensemble of Gene Set Enrichment Analyses (EGSEA) for count matrix generated by DESeq2 and edgeR packages
RNA-Seq EGSEA GSEA DESeq2 edgeR
updated 4.1 years ago by 20 • written 4.7 years ago by ▴ 80
0
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2
replies
745
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How to detect novel proteins and non-annotated proteins from a list of MS proteins?
mass spectrometry proteomics novel proteins
4.2 years ago by Farah ▴ 80
1
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0
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1.9k
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How to modify bin interval and bars colour in a bar polar chart created by plotly package in R?
plotly R bar_polar_chart Radial_histogram
4.3 years ago by Farah ▴ 80
0
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0
replies
1.1k
views
How to make a quarter circle polar plot using ggplot2?
ggplot2 coord_polar R quarter-circle-polar-plot
4.3 years ago by Farah ▴ 80
2
votes
2
replies
1.3k
views
How to modify the nodes features in Gradient1 style in Cytoscape?
Cytoscape String 3D Gradient1
updated 4.4 years ago by ▴ 540 • written 4.4 years ago by ▴ 80
1
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2
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1.4k
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How to interpret a Stringdb interaction network of a mouse-proteomics dataset when it is detected only in Homo sapiens organism?
Stringdb interaction proteomics network String
updated 4.4 years ago by 6.5k • written 4.4 years ago by ▴ 80
12
votes
7
replies
4.2k
views
Graphical presentation of STRING protein-protein network and gene ontology
STRING DAVID gene-ontology interaction-network
updated 4.4 years ago by ★ 1.3k • written 4.4 years ago by ▴ 80
2
votes
1
reply
893
views
protein-protein interaction network
String network interaction
4.4 years ago by Farah ▴ 80
16
votes
8
replies
14k
views
Confusion about FindMarkers(), FindVariableFeatures(), RunTSNE(), and RunUMAP() in seurat package
scRNA-seq kallisto Seurat bustools
updated 13 months ago by 43k • written 4.5 years ago by ▴ 80
2
votes
8
replies
3.8k
views
How to make a loop to run kallisto bus command for so many fastq.gz files at once?
bash kallisto bustools
updated 13 months ago by 43k • written 4.5 years ago by ▴ 80
3
votes
6
replies
3.7k
views
How to install bamtofastq utility in my terminal?
kallisto bamtofastq bustools
updated 13 months ago by 43k • written 4.5 years ago by ▴ 80
3
votes
6
replies
1.2k
views
Is "Attribute Circle Layout" of a protein-protein network standard and acceptable for a good publication?
cytoscape network interaction
updated 4.5 years ago by ▴ 620 • written 4.6 years ago by ▴ 80
1
vote
7
replies
2.5k
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Kallisto | bustools workflow for fastq with R1 and R2 (forward and reverse)?
scRNA-seq Kallisto bustools
updated 13 months ago by 43k • written 4.6 years ago by ▴ 80
2
votes
7
replies
2.9k
views
Converting Ensembl gene IDs to Entrez IDs for indexing gene set collections for doing "Ensemble of Gene Set Enrichment Analyses"
RNA-Seq edgeR EGSEA limma biomaRt
updated 4.6 years ago by 43k • written 4.6 years ago by ▴ 80
1
vote
2
replies
6.2k
views
Error in tximport: all(file.exists(files)) is not TRUE
tximport DESeq2
updated 4.7 years ago by 35k • written 4.7 years ago by ▴ 80
5
votes
9
replies
3.0k
views
How to change my colnames(count.table) as exactly similar to my rownames(meta)?
RNA-Seq Kallisto DESeq2 R tximport
updated 4.7 years ago by 81k • written 4.7 years ago by ▴ 80
4
votes
4
replies
1.9k
views
How to quantify the RNA-seq reads using Kallisto?
RNA-Seq Kallisto
updated 4.7 years ago by 43k • written 4.7 years ago by ▴ 80
3
votes
9
replies
12k
views
Build a Kallisto transcriptome index
Kallisto RNA-Seq pseudo-alignment
updated 4.8 years ago by ▴ 700 • written 4.8 years ago by ▴ 80
4
votes
13
replies
1.7k
views
Running Trimmomatic for bulk RNAseq data
RNA-Seq Trimmomatic FastQC
4.8 years ago by Farah ▴ 80
1
vote
4
replies
2.8k
views
Running SortMeRNA for bulk RNAseq data
sortmerna RNA-Seq
updated 10 months ago by 43k • written 4.8 years ago by ▴ 80
3
votes
3
replies
6.6k
views
How to download RNA-seq dataset (fastq.gz files) from GEO and SRA databases?
fastq SRA RNA-Seq GEO
updated 13 months ago by 43k • written 4.8 years ago by ▴ 80
0
votes
2
replies
1.2k
views
How to create plots correlating mRNA expression with PAM50 and my bait protein's expression using cBioPortal database?
cBioPortal PAM50 assay mRNA expression
4.8 years ago by Farah ▴ 80
4
votes
9
replies
2.7k
views
How to install SortMeRNA tool on my university HPC cluster?
RNA-Seq HPC Cluster cluster computing
updated 4.9 years ago by ★ 2.2k • written 4.9 years ago by ▴ 80
0
votes
6
replies
2.4k
views
How to mount my data into docker container through -v command?
rna-seq docker container bash scripting
4.9 years ago by Farah ▴ 80
0
votes
4
replies
1.9k
views
Difficulty in opening downloaded stringApp.jar file
Cytoscape jar plugin stringApp Cytoscape plugin
updated 5.2 years ago by ▴ 620 • written 5.2 years ago by ▴ 80
32 results • Page 1 of 1
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