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Job: Data Engineer / Bioinformatician- AZ-Crick-Imperial College: Molecular Glue Discovery Partnership
data-engineering drug-discovery data-science
updated 14 hours ago by 39k • written 1 day ago by ▴ 220
0
votes
4
replies
199
views
variant allelic fraction
vep
7 hours ago by malm • 0
0
votes
2
replies
160
views
WGCNA Trait File Issues
correlation Deseq2 Gene WGCNA
updated 1 day ago by 2.6k • written 1 day ago by • 0
0
votes
1
reply
137
views
Pairwise Alignment
Pairwise-Alignment
updated 14 hours ago by 39k • written 1 day ago by • 0
3
votes
6
replies
2.0k
views
h5ad cellxgene to R
single-cell h5 cellxgene anndata R
updated 1 day ago by 129k • written 6 months ago by ★ 1.5k
4
votes
5
replies
315
views
calculate p value and associated z score for snp-gene pair
snp association gene pvalue
updated 10 hours ago by 2.6k • written 3 days ago by ▴ 140
1
vote
3
replies
318
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What is the benefit of knowing the source of contamination when we have RNAseq data with less than 70% mapping?
alignment mapping STAR contamination RNAseq
1 day ago by Sib ▴ 40
0
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0
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90
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How to perform a phylogenetic analysis from a vcf file
variants haplotyping phylogeny vcf
1 day ago by rj.rezwan • 0
0
votes
1
reply
152
views
Where to get the molecular subtype information of STAD sample in TCGA
TCGA database
updated 1 day ago by 2.9k • written 1 day ago by ▴ 50
0
votes
2
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223
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Filtering mitochondrial reads from ATAC-Seq aligned reads- what to do with reads that have MT in RNEXT field
RNEXT filtering mitochondrial_reads ATAC-Seq samtools
updated 1 day ago by 3.6k • written 2 days ago by • 0
1
vote
5
replies
346
views
Is a human genome file with reference as NCBI37 the same as hg19?
vcf hg19 genome reference-genome
updated 1 day ago by 129k • written 2 days ago by • 0
5
votes
4
replies
378
views
Forum: [Meta] Use of AI
AI Artificial-Intelligence meta ChatGPT
updated 14 hours ago by 39k • written 2 days ago by ★ 2.9k
0
votes
0
replies
130
views
How to keep ComplexHeatmap from reordering annotations
Dendrogram HeatmapAnnotations R Heatmap ComplexHeatmap
2 days ago by Manuel • 0
3
votes
5
replies
385
views
RNASeq gene labeling and mRNA filter from bulkRNA data.
RNA-Seq RSubreads
updated 3 hours ago by ▴ 140 • written 4 days ago by • 0
1
vote
2
replies
244
views
Random dataset and DESeq2
DESeq2
updated 2 days ago by ★ 2.9k • written 2 days ago by • 0
1
vote
1
reply
214
views
Network cross-validation
wgcna RNASeq Network CV
updated 2 days ago by 2.6k • written 2 days ago by ▴ 500
0
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0
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126
views
Differential protein expression analysis
R proteomic statistics
2 days ago by Ribo ▴ 40
0
votes
3
replies
304
views
(ERR): "index/Trinity.fa" does not exist or is not a Bowtie 2 index Exiting now ...
bowtie2 align_stats trinity
1 day ago by eimanpharmacist ▴ 20
1
vote
2
replies
231
views
I have one fasta file of a bacteria. Can i use to create a phylogenetic tree?
Bioinformatics WGS
2 days ago by Mustafa • 0
0
votes
4
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347
views
What are recommended parameters for the local protein alignment ?
protein alignment
1 day ago by Alexander ▴ 70
0
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0
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122
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microsatellite, SSR, using Galaxy
Galaxy SSR using microsatellite
2 days ago by m.esmaeilpour ▴ 10
2
votes
2
replies
262
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integrate single cell RNA sequencing data
scRNAseq single-cell
updated 3 days ago by 2.9k • written 3 days ago by ▴ 50
0
votes
0
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139
views
decoupleR & Transcription Factory Activity Inference: pvalue or padj?
pvalue padj decoupleR
3 days ago by OST ▴ 10
3
votes
7
replies
420
views
How to sort gff3 according to chromosome order?
gff3 sort
updated 3 days ago by 154k • written 3 days ago by • 0
2
votes
3
replies
326
views
Low mapping percentage
mapping STAR RNAseq
2 days ago by Sib ▴ 40
0
votes
0
replies
165
views
Visualization App for RNASeq Differential Expression and Enrichment Analysis
differential visualization RNASeq analysis expression enrichment
3 days ago by Mark • 0
4
votes
3
replies
297
views
What does canonical transcript mean in the context of VEP
vep
updated 3 days ago by ★ 2.9k • written 3 days ago by ▴ 720
0
votes
0
replies
185
views
Job: Postdoctoral Research Associate in bio-ontologies and machine learning (Imageomics)
Machine-Learning PostDoc Data-Science Biology Ontology
updated 3 days ago by 39k • written 3 days ago by • 0
3
votes
4
replies
279
views
bcftools "--filter-logic" flag, what + means?
bcftools vcf
updated 22 hours ago by ▴ 360 • written 3 days ago by ▴ 170
0
votes
0
replies
155
views
busco id description
OrthoDB BUSCO
updated 3 days ago by 39k • written 3 days ago by • 0
0
votes
5
replies
376
views
how to Construct a Newick tree file from five large fasta files
tree Newick alignment
updated 3 days ago by 21k • written 3 days ago by • 0
2
votes
7
replies
481
views
What is "pident" (percentage of identical matches) in the "Diamond" protein alignment ?
protein alignment
updated 3 days ago by ★ 2.9k • written 3 days ago by ▴ 70
0
votes
0
replies
161
views
NMDS plotting issue
NMDS metagenomic
3 days ago by arshad1292 ▴ 90
0
votes
2
replies
225
views
featurecounts not working on mirbase annotation file
usegalaxy miRNA-seq
9 hours ago by demoraesdiogo2017 ▴ 90
0
votes
0
replies
149
views
News: Generalized Linear Models (GLM) course in R
R GLM statistics
3 days ago by carlopecoraro2 ★ 2.3k
0
votes
0
replies
137
views
IGV insertions
insertions IGV
3 days ago by christoph.schubart • 0
1
vote
0
replies
147
views
Bayesian network for biological data using bnlearn
bnlearn RNA-seq bayesian-network
updated 3 days ago by 39k • written 3 days ago by ▴ 10
0
votes
0
replies
144
views
jellyfish options
kmer jellyfish
3 days ago by Tele • 0
0
votes
1
reply
417
views
Diffbind not calling sites as differentially bound
DiffBind
updated 3 days ago by ★ 1.7k • written 9 months ago by • 0
0
votes
3
replies
215
views
hardfilter error
bam recall
3 days ago by bestone ▴ 10
0
votes
1
reply
182
views
Creating a local version of Clustered NR database
diamond clustered-nr blast
updated 3 days ago by 39k • written 3 days ago by • 0
0
votes
1
reply
284
views
News: 7th Berlin Summer School in NGS Data Analysis (September 4-8 in Berlin)
Variant-Calling Transcriptomics RNA-Seq DNA-Seq
updated 3 days ago by 39k • written 28 days ago by 9.9k
0
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0
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118
views
cnetplot enrichment graph to cytoscape
clusterprofiler cnetplot enrichplot
3 days ago by Omics data mining ▴ 220
0
votes
0
replies
121
views
How to extract the surrogate variables from DNA methlation Data
sva array limma methylation
updated 3 days ago by 129k • written 3 days ago by • 0
1
vote
1
reply
572
views
Reads with highest MAPQ values from SAM files are showing mismatches to reference sequence and IGV classified them as supplementary reads
minimap Nanopore IGV
updated 3 days ago by 129k • written 3 days ago by ▴ 20
0
votes
5
replies
306
views
All combinations of two columns R
R
updated 3 days ago by 39k • written 3 days ago by • 0
0
votes
0
replies
118
views
Stratified sample assignment for analysis
experimental-design stratification
updated 3 days ago by 39k • written 3 days ago by ▴ 200
0
votes
0
replies
113
views
Convert tree into bifurcation table
Tree Newick ASR Mutation
3 days ago by Alexandre • 0
0
votes
1
reply
174
views
how to call variants in haploid genome
haploid-genome
updated 3 days ago by 39k • written 4 days ago by • 0
0
votes
1
reply
177
views
Processing WES VCF for case control GWAS analysis
GWAS PLINK
updated 3 days ago by ▴ 360 • written 3 days ago by • 0
1,000 results • Page 2 of 20
Recent Votes
A: Why do PCA+tSNE/viSNE or PCA+UMAP, and not just tSNE/viSNE or UMAP on their own?
A: Why do PCA+tSNE/viSNE or PCA+UMAP, and not just tSNE/viSNE or UMAP on their own?
Why do PCA+tSNE/viSNE or PCA+UMAP, and not just tSNE/viSNE or UMAP on their own?
Comment: Help with running ATAC using Encode pipeline
Answer: Finding Enhancers using Genomation library
Comment: Is my estimated genome coverage correct?
Answer: How to calculate TPM from featureCounts output
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Recent Replies
Answer: Get relationships and hierarchies for GO terms by rfran010 ▴ 140
Maybe stringdb? seems to have an option to do what you describe. https://string-db.org/cgi/input?sessionId=bmYwdg48WePq&input_page_activ…
Comment: How to calculate TPM from featureCounts output by rfran010 ▴ 140
This file is your counts file, isn't it?
Comment: Help with running ATAC using Encode pipeline by rfran010 ▴ 140
Curious, can you give specific examples of what you refer to as "input file" and "json file"? In the screenshot you shared, input files re…
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data. by rfran010 ▴ 140
What version are you running? I use v2.0.3 on the command line. It looks like this option may be added in a later version, with `GTF.attrT…
Answer: Get relationships and hierarchies for GO terms by Vincent Laufer ★ 2.9k
Hey Daniel, **First, one potential caveat.** Above, you say "I have obtained several GO terms (indicating function and biological proc…
Comment: Perl. How to retrieve data until a keyword in GenBank? by Fungi-Beware! ▴ 10
THANK YOU!! Your method works!! And by removing: $data = ''; I figured out how to retrieve the annotation info with a prompt: …
Comment: variant allelic fraction by malm • 0
Ok but i have only vep files i don't have vcf files
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data. by Yeeshouw • 0
Yes, I am inputting a GTF file. I reviewed the `[featureCounts][1]` documentation, and I could not find this `extraAttributes` parameter. …
Comment: Italicise annotations with pheatmap by jamie.pike ▴ 80
@ATpoint Very true! I'm not so familiar with many image editing software and I wonder if it will be just as quick for me to try in R, but I…
Comment: Italicise annotations with pheatmap by jamie.pike ▴ 80
You're right, I was trying to save time and not write for in ComplexHeatmap, but using @Trivas ComplexHeatmap::pheatmap() should help! Than…
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data. by Yeeshouw • 0
Thank you very much for information! I am able to see this column you mention.
Comment: Italicise annotations with pheatmap by ATpoint 72k
I might be the party pooper but I generally think that these sorts of aesthetics should be done later in something like Inkscape. In R do t…
Comment: Embryo transcriptome by ATpoint 72k
Just one, that is how the convention is. One sample (SRX...) can have one or many SRR entries. If many you can merge them prior to quantifi…
Comment: What kind of statistical test does Cellranger count use? by ATpoint 72k
Clustering is not a statistical test with p-values. It is unclear what you mean. Actually, I would just ignore everything that the blackbox…
Comment: Information on sequin RNA spike in standards by Ram 39k
I'd try emailing the authors for a link.
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