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Bioinformatics

Revival

 Revival
Answer more than 30 days after a question was asked as first answer scoring 2 or more. This badge can be awarded multiple times.
Awarded 194 times.
Cox model with percentage interpretation
Awarded Nov 13 at 15:07
What is a 'structure' and a 'model' in BioPython?
Awarded Nov 8 at 6:41
Fragment mass tolerance in proteomics analysis
Awarded Nov 1 at 17:15
Issue with iCTNet2 installation
Awarded Jul 5 at 5:27
Cytoscape for coloring the nodes in the network
Awarded Jul 5 at 5:27
Convert ensemble genes to gene names in my sigle cell signature matrix annotated with seurat in R?
Awarded Jun 3 at 16:07
Proper formatting of .ped files, in order to run ADMIXTURE
Awarded May 9 at 17:45
How to import data from cell ranger to R (Seurat)?
Awarded May 2 at 17:56
How to perform liftover from 38 to 37 in R?
Awarded Apr 4 at 19:42
Can alphafold 2 be used to identify residues important for binding?
Awarded Apr 4 at 17:47
How to compute LD for pairs of variants with Plink
Awarded Mar 24 at 16:42
Merge / Reconciliate several de novo transcriptome assemblies with different kmers
Awarded Mar 14 at 11:50
Bar Graph of Expression Data from Seurat Object
Awarded Feb 15 at 16:00
Converting convert .svs files into .mrxs format
Awarded Jan 19 at 16:16
Featureplot by co-expression of some genes
Awarded Jan 9 at 12:05
Where can I find lncRNA expression data for different cell types?
Awarded Dec 12, 2023 at 17:33
annotation using ChIPseeker package error
Awarded Dec 4, 2023 at 18:16
Why are TPMs per 10k or 100k in many scRNA-seq studies?
Awarded Nov 27, 2023 at 14:16
(post deleted or otherwise unavailable)
Awarded Nov 13, 2023 at 22:05
How to get cytoband and gene level copy number from genome wide SNP array copy number data?
Awarded Nov 1, 2023 at 23:41
What samples can be used for a Mutect2 Panel of Normals
Awarded Oct 30, 2023 at 6:32
How to do average macrophages signature boxplots, with Bulk RNA data from 2 control and 2 treatment samples and LM22 signature matrix from cibersort?
Awarded Oct 25, 2023 at 20:04
LD clump GRCh38 GWAS results
Awarded Oct 21, 2023 at 8:00
How to get a MSA fasta from BAM/SAM?
Awarded Oct 9, 2023 at 18:49
Extract data from genome
Awarded Oct 9, 2023 at 15:16
Biopython - extracting query coverage from XML Blast output
Awarded Oct 9, 2023 at 9:13
Why do we delete scaffolds shorter than 500 - 1000 bp from the assembled genome?
Awarded Oct 9, 2023 at 0:50
How to remove black outline from Seurat's VlnPlot violin plot
Awarded Oct 7, 2023 at 22:28
Blastp MSA to the same length
Awarded Sep 13, 2023 at 17:11
Minfi and estimateCellCounts Error: in p[trainingProbes, ]: subscript out of bounds
Awarded Aug 18, 2023 at 22:07
How to convert Foldseek .m8 alignment files to FASTA format?
Awarded Aug 8, 2023 at 12:12
Run nextflow pipeline multiple times depending on length of a list
Awarded Jul 26, 2023 at 16:35
Is there any function in Biopython to convert a DNA sequence from ambiguous to unambiguous?
Awarded Jul 23, 2023 at 12:07
Is there any function in Biopython to convert a DNA sequence from ambiguous to unambiguous?
Awarded Jul 14, 2023 at 18:55
Percentage of each cluster in Seurat
Awarded Jul 10, 2023 at 14:02
Retrieving NCBI Taxa IDs from refseq or GenBank assembly accession
Awarded Jul 4, 2023 at 5:46
How do I lift GWAS results to hg38?
Awarded Jun 15, 2023 at 23:28
Identification of unique chains in proteins by sequence similarity
Awarded Jun 7, 2023 at 16:16
Negative binomial modeling of RNA-Seq data
Awarded May 20, 2023 at 23:08
lower mapping rates in salmon v0.13 compared to previous versions
Awarded Apr 3, 2023 at 13:17
How do I include silent mutations in an oncoplot using maftools?
Awarded Mar 28, 2023 at 18:22
Is it possible to create SMILES representation out of DNA/RNA-Oligonucleotides (~50 nts)?
Awarded Mar 17, 2023 at 22:16
Normalization using parallel R script
Awarded Mar 1, 2023 at 17:45
Making a bed file for RSeQC
Awarded Mar 1, 2023 at 6:56
Different results in differential expression analysis of microarray data
Awarded Feb 3, 2023 at 14:58
Ubiquitous regulation of highly specific marker genes
Awarded Dec 18, 2022 at 11:19
Why does this modification site file contain duplicate sites and multiple related proteins?
Awarded Dec 16, 2022 at 16:18
Ubiquitous regulation of highly specific marker genes
Awarded Dec 16, 2022 at 12:47
Concatenate multiple fasta files into one file for MLST
Awarded Dec 7, 2022 at 9:35
Given a multiple sequence alignment, how do I output all of the non-consensus characters by location?
Awarded Nov 30, 2022 at 15:09
Any way to filter out highly correlated genes with limma linear model?
Awarded Nov 18, 2022 at 20:32
bedtools coverage - Report the depth at each position in each A feature
Awarded Nov 17, 2022 at 18:01
Voom function from limma package and Normalization on counts data
Awarded Nov 9, 2022 at 13:17
include a glimma interface in a shiny app
Awarded Oct 1, 2022 at 5:57
Methylation data: beta values are normally distributed
Awarded Sep 22, 2022 at 14:27
Downloading genomic protein files from accessions in Python
Awarded Sep 22, 2022 at 4:18
What is the difference between AnnotationDbi/org.Mm.eg.db and biomaRt/Mus.musculus for converting to gene symbols?
Awarded Aug 18, 2022 at 21:16
How to extract clusters from a phylogenetic tree?
Awarded Aug 17, 2022 at 7:50
Permutations of 4 amino acid sequence oligopeptide
Awarded Aug 7, 2022 at 21:11
Pymol: select low confidence regions from AlphaFold pdb file
Awarded Jul 22, 2022 at 17:17
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