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Showing top results for tag: clustering • reset
4
votes
4
replies
226
views
  distance matrix as input in R clustering functions ?
k-medioids-genetic-distances-mash R Clustering
updated 3 days ago by 24k • written 9 days ago by ▴ 30
0
votes
0
replies
54
views
  Differentiating alleles from paralogs in comparison of transcriptomes within species
clustering transcriptome paralog trinity assembly
20 days ago by jfaberha ▴ 10
2
votes
2
replies
230
views
  Why clusters look different in single nuclear RNA Seq.
snRNA clustering seurat
updated 4 weeks ago by 74k • written 4 weeks ago by ▴ 10
2
votes
1
reply
267
views
  how to define open-pangenome?
python fasta genome dna clustering
updated 6 weeks ago by ▴ 20 • written 12 weeks ago by ▴ 50
0
votes
1
reply
101
views
  Hierarchical clustering using GISTIC 2.0 result
clustering CNV hierarchical GISTIC CNA
updated 6 weeks ago by ★ 2.3k • written 6 weeks ago by • 0
0
votes
0
replies
68
views
  Supervised clustering from gene expression (fold change) data
clustering expression supervised
7 weeks ago by nerea.bilbao • 0
1
vote
1
reply
113
views
  RMSD clustering
Clustering
updated 7 weeks ago by ★ 11k • written 7 weeks ago by • 0
0
votes
2
replies
137
views
  Clustering 10X scRNA data based on selected markers
clustering scRNA seurat umap pca
7 weeks ago by A • 0
22
votes
4
replies
2.9k
views
Tutorial:  A simple tutorial for a complex ComplexHeatmap
complexheatmap clustering arthritis pam Tutorial
updated 9 weeks ago by ▴ 60 • written 13 months ago by 74k
5
votes
3
replies
3.0k
views
Tool:  Clustering of short peptide sequences
peptide clustering phage display Tool
updated 9 weeks ago by • 0 • written 5.7 years ago by ▴ 400
7
votes
12
replies
883
views
  RNAseq data analysis of pooled data
DESeq2 mapping featurecounts clustering RNA-Seq
updated 9 weeks ago by ★ 2.2k • written 10 weeks ago by ▴ 20
4
votes
3
replies
370
views
  Hierarchical Clustering of GO terms
Clustering GO similarity Ontology
updated 10 weeks ago by 74k • written 10 weeks ago by ▴ 160
0
votes
0
replies
168
views
News:  3-day ONLINE TRAINING - NEXTFLOW
pipeline programming workflow cloud clustering
updated 12 weeks ago by 103k • written 12 weeks ago by ★ 2.0k
3
votes
2
replies
511
views
  Pheatmap/Complexheatmap: making a continuous color scale with NAs
clustering pathways complexheatmap pheatmap
12 weeks ago by Ridha ▴ 40
0
votes
7
replies
603
views
  Cannot resize rowlabels in aheatmap
clustering aheatmap R
updated 12 weeks ago by 5.3k • written 12 weeks ago by • 0
5
votes
4
replies
484
views
  Interpretation of Principal component analysis
clustering
updated 12 weeks ago by ★ 11k • written 3 months ago by • 0
1
vote
2
replies
300
views
  Clustering two different RNA-seq timeseries results to identify shared/opposite gene patterns?
RNA-seq trajectories timeseries clustering
10 weeks ago by kelen ▴ 170
0
votes
0
replies
145
views
  Identify cell type from bulk RNA sequencing data
sequencing type clustering r
3 months ago by minoo ▴ 10
0
votes
0
replies
209
views
  Does anyone succeded clustering TCGA data?
RNA-Seq TCGA clustering
updated 3 months ago by 20 • written 4 months ago by • 0
1
vote
1
reply
191
views
  determine the robustness of single-cell clusters
clustering RNA-Seq rna-seq R Seurat
updated 3 months ago by ▴ 180 • written 3 months ago by • 0
0
votes
0
replies
166
views
  Cluster Stability Assesment
rna-seq Seurat clustering R
3 months ago by Maria17 • 0
3
votes
5
replies
186
views
  Clustering sequences with low identity
clustering sequences
updated 4 months ago by ★ 11k • written 4 months ago by ▴ 810
1
vote
3
replies
231
views
  How to run nucmer without reference? (viruses metagenomics)
assembly clustering metagenomics virus nucmer
updated 4 months ago by ★ 2.9k • written 4 months ago by ▴ 150
3
votes
5
replies
463
views
  Is my WGCNA soft threshold (power) too low?
wgcna RNA-Seq clustering network
4 months ago by jfaberha ▴ 10
0
votes
0
replies
231
views
  Using ATACseq CPM for clustering samples
ATAC-seq normalization clustering
5 months ago by barati • 0
6
votes
5
replies
330
views
  CD-HIT: representative sequence vs consensus sequence
CD-HIT clustering
5 months ago by rob_DNA ▴ 10
0
votes
0
replies
213
views
  Cluster sequences in a network by their editing distance - in R
R network analysis clustering editing distance
5 months ago by fendermannn • 0
0
votes
1
reply
255
views
  How to select the number of clusters once I have the HCL (average linkeage) tree
hierarchical clustering gene co-expression
6 months ago by sofiablancoglez • 0
1
vote
1
reply
635
views
  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 6 months ago by ▴ 450 • written 6 months ago by ▴ 70
2
votes
11
replies
7.1k
views
7 follow
  CD-HIT Clustering output
CD-HIT Clustering
updated 6 months ago by ▴ 70 • written 6.9 years ago by • 0
0
votes
0
replies
309
views
  Analyze RPPA cancer data in R for clustering patients and differential protein expression
RPPA RPPanalyzer R clustering DE
7 months ago by svlachavas ▴ 740
3
votes
3
replies
260
views
  Clustering similiar genes from many genomes
Python genome pangenomics clustering
updated 7 months ago by 19k • written 7 months ago by • 0
0
votes
4
replies
281
views
  identification of rare cell population in Sc-RNA sequencing
rna-seq R clustering rare population seurat
7 months ago by Maria17 • 0
1
vote
2
replies
297
views
  How to do unsupervised clustering of RNA-Seq data
RNA-Seq clustering next-gen
7 months ago by Kumar ▴ 100
2
votes
1
reply
397
views
  Correlating metadata with expression based k-means cluster (in R)
R k-means clustering
updated 7 months ago by ▴ 940 • written 10 months ago by ▴ 230
1
vote
2
replies
331
views
  optimal number of clusters from distance matrix input
clustering R
updated 8 months ago by 74k • written 8 months ago by ▴ 90
0
votes
4
replies
410
views
  Interpretation of two PCA plots
RNA-Seq pca clustering
updated 8 months ago by 10k • written 8 months ago by ▴ 90
2
votes
10
replies
320
views
  How to identify which genes are responsible for the different cluster without PCA
R hclust clustering bulkRNAseq
updated 8 months ago by 7.2k • written 8 months ago by ▴ 40
0
votes
2
replies
415
views
  Visualise CD-HIT clusters?
clustering data visualisation CD-HIT
updated 8 months ago by 20 • written 10 months ago by ▴ 80
2
votes
1
reply
415
views
  Scaling RNA-Seq data before clustering?
RNA-Seq Clustering Hierarchical clustering Scaling
updated 8 months ago by 50k • written 8 months ago by • 0
0
votes
3
replies
285
views
  Differencial expression analysis between groups determined by two variables
expression microarray clustering
8 months ago by jeni ▴ 50
8
votes
11
replies
2.7k
views
  How many PCs should be considered for downstream analyses?
scRNAseq PCA UMAP Clustering RNAseq
updated 8 months ago by ▴ 120 • written 16 months ago by ▴ 280
6
votes
6
replies
3.1k
views
  Clustering of genes using FPKM
RNA-Seq clustering FPKM R bioconductor
updated 9 months ago by ★ 1.5k • written 6.5 years ago by ★ 1.1k
1
vote
7
replies
1.2k
views
  Result of scanpy tools rank_genes_groups
gene scanpy seurat rank_gene_groups clustering
updated 9 months ago by • 0 • written 13 months ago by ▴ 20
2
votes
5
replies
664
views
  Best package to cluster a single cell dataset using marker gene lists retrieved from elsewhere?
RNA-Seq single cell sequencing clustering
updated 9 months ago by ▴ 20 • written 19 months ago by ▴ 10
0
votes
0
replies
240
views
  individual-level allele frequencies
allele frequencies clustering plink
9 months ago by anamaria ▴ 160
5
votes
3
replies
555
views
  Which is the proper RNA-seq count table transformation to perform hierarchial clustering analysis?
RNA-Seq stats clustering
updated 10 months ago by ★ 2.2k • written 10 months ago by ★ 2.1k
0
votes
1
reply
269
views
  Export CLANS clusters in separate multifasta files
CLANS clustering FASTA
updated 10 months ago by 20 • written 11 months ago by ▴ 10
2
votes
2
replies
381
views
  error in hcluster although there is no NA/NAN/infinite
R Heatmap clustering
updated 11 months ago by 24k • written 11 months ago by ▴ 100
0
votes
1
reply
791
views
  Converting mouse Ensembl ID's to gene names in a data frame
RNA-Seq R biomart pheatmap clustering
updated 11 months ago by 74k • written 11 months ago by • 0
50 results • Page 1 of 1
Recent Votes
Comment: MERLIN: skipped due to megabytes problem
Comment: MERLIN: skipped due to megabytes problem
Duplicate genotypes after phasing in Beagle
Answer: Beagle: Skip intervals with no common markers
A: How Do You Manage Your Files & Directories For Your Projects ?
A: How Do You Manage Your Files & Directories For Your Projects ?
Snakemake error: "Removing output files of failed job since they might be corrupted:"
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Comment: Beagle: Skip intervals with no common markers by Jack ▴ 10
sorry I forgot to clarify, in the example `beagle` is an alias for `java -Xmx50g -jar beagle.25Nov19.28d.jar`
Comment: Biopython's Esearch for Pubmed does not give the same results as web search by GenoMax 103k
To follow up on this - Entrezdirect seems to be doing an "All Fields" search by default. $ esearch -db pubmed -query "sclerosis" <…
Comment: Local realignment around indels by Pierre Lindenbaum 136k
when publishing it's (sadly?) better to say you used the "GATK best practices" to call your variants...
Comment: MERLIN: skipped due to megabytes problem by 349151519 • 0
Thank you so much for replying. I reduced my pedigree size and it worked. : )
Comment: MERLIN: skipped due to megabytes problem by 349151519 • 0
Thank you so much for replying. I reduced my pedigree size and it worked. : )
Comment: IPA - gene list by GenoMax 103k
That information is generally shown in tables etc. Number of genes from your list that are present in the pathway.
Comment: How to create a proper design matrix/contrast matrix for methylation 850k analys by i.sudbery 12k
This is a not an answer to the above question, please open a new question.
Comment: IPA - gene list by shreya.kouda • 0
Is there a way to export just the genes from our dataset? I do not want all the genes from the pathway, rather just the genes that are part…
Answer: Different ab initio 3D structure prediction for same protein sequence by trRoset by jgreener ▴ 330
Have a read of the trRosetta paper and the section "Structure Determination by Energy Minimization with Predicted Restraints" will give you…
Comment: Local realignment around indels by Elisa • 0
I was calling the variants with bcftools. Do you suggest me to use GATK4 instead? (I have a targeted sequencing problem with tumor samples)
Answer: Biopython's Esearch for Pubmed does not give the same results as web search by lbehringer • 0
I can think of two factors that might cause different results between Biopython and the web search: 1. Depending on how specific the query…
Answer: Local realignment around indels by Pierre Lindenbaum 136k
> I should perform local realignment only after PCR duplicates removal? if you're calling the variant with GATK4, you don't need to rea…
Comment: How to calculate the difference between the RNA-Seq individual samples? by mohammedtoufiq91 ▴ 110
@seidel, thank you very much.
Comment: How to create a proper design matrix/contrast matrix for methylation 850k analys by almsu798 • 0
Hi, what if you have 20 patients and for each patient you have two sources of tissues (Primary and metastatic). I have tried the below but …
Answer: Snakemake error: "Removing output files of failed job since they might be corru by dariober 12k
`diff` returns exit code 1 if the files differ and that makes snakemake throw the error you see. Similar behaviour happens if `grep` doesn'…
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