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4.0k
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Converting mouse Gene IDs to Human while keeping genes that don't convert
bioMart RNA-seq Bioconductor R
4.2 years ago by oludhe ▴ 90
0
votes
1
reply
792
views
Histone marks enrichment analysis
RNA-Seq
updated 4.2 years ago by ▴ 520 • written 4.2 years ago by ▴ 10
2
votes
1
reply
4.1k
views
MinION Data Examples (FAST5) Database
ONT FAST5 MinION DNA
updated 4.2 years ago by 154k • written 4.2 years ago by ▴ 200
0
votes
6
replies
4.4k
views
computematrix how to set certain TSS
deeptools
4.2 years ago by Binghong ▴ 20
0
votes
0
replies
896
views
Error in haploview data format
haploview
updated 4.2 years ago by 45k • written 4.2 years ago by • 0
5
votes
5
replies
2.7k
views
Integrated Dimension Reduction Plot for CD4/CD8 sorted Feedback
10x seurat immunology
updated 4.2 years ago by ▴ 280 • written 4.3 years ago by ▴ 40
1
vote
1
reply
1.5k
views
Corelate TCR data to clusters/GEX/CITEseq data
10x vdj tcr seurat
updated 4.2 years ago by ▴ 280 • written 4.3 years ago by ▴ 40
1
vote
1
reply
1.4k
views
Analyzing TCRseq Data
tcr TCRseq scRepetoire Immunarch
updated 4.2 years ago by ▴ 280 • written 4.6 years ago by ▴ 90
0
votes
0
replies
770
views
Job: PDRA in Computational Biophysics and Cancer Research, University of Manchester, UK
Structural-Genomics pH-dependence Cancer
updated 2.6 years ago by 45k • written 4.2 years ago by • 0
2
votes
1
reply
1.3k
views
Forum: Advise for a computational neophyte
education research thesis master topic
updated 4.2 years ago by 4.1k • written 4.2 years ago by • 0
0
votes
0
replies
864
views
Relative abundance of differentially abundant ASVs after DESeq2
DESeq2 ASV
updated 4.2 years ago by 45k • written 4.2 years ago by • 0
1
vote
9
replies
2.2k
views
microarray miRNA expression data analysis
microarray R
updated 4.2 years ago by 89k • written 4.2 years ago by ▴ 20
2
votes
3
replies
5.7k
views
Functional enrichment analysis of bacteria
GO enrichment DAVID bacteria clusterProfiler R
updated 4.2 years ago by ★ 2.6k • written 4.9 years ago by ▴ 110
3
votes
8
replies
5.4k
views
How to search dbSNP using a list of SNPs and retrieve Gene name (hgnc symbol if existing, otherwise just whatever is in there)
biomaRt R
updated 3.8 years ago by ▴ 70 • written 4.5 years ago by ▴ 10
0
votes
3
replies
1.4k
views
Antibody Matching Transcripts
GeneralIdentifiers isoforms Antibody ensembl HumanAtlasProtein
updated 4.2 years ago by ★ 2.4k • written 4.2 years ago by ▴ 50
11
votes
5
replies
2.8k
views
6 follow
Beginner level projects for bioinformatics.
data-science Python
updated 4.2 years ago by 45k • written 4.2 years ago by ▴ 80
26
votes
6
replies
7.2k
views
9 follow
Forum: Making a living with bioinformatics
career
updated 3.3 years ago by 45k • written 7.4 years ago by ▴ 150
2
votes
4
replies
5.2k
views
relevel the clusterProfiler object
clusterProfiler
4.2 years ago by grant.hovhannisyan ★ 2.6k
2
votes
12
replies
8.0k
views
How to get KEGG pathway names in KEGG enrichment analysis using clusterprofiler
annotation enrichment KEGG clusterprofiler RNA-Seq
updated 4.2 years ago by ★ 2.6k • written 5.5 years ago by ▴ 190
0
votes
0
replies
564
views
TCGA WXS positions covered
WXS TCGA coverage
4.2 years ago by s.cleary12 • 0
2
votes
7
replies
6.6k
views
clusterProfiler and enrichplot: visualising groupGO results with individual genes and their fold changes
clusterProfiler enrichplot
updated 4.2 years ago by ★ 2.6k • written 4.6 years ago by • 0
0
votes
2
replies
2.2k
views
GO enrichment analysis in R on Solanum lycopersicum proteomics dataset
R GeneOntology GO clusterprofiler UNIPROT
updated 4.2 years ago by ★ 2.6k • written 4.7 years ago by • 0
0
votes
1
reply
714
views
Why sometimes map all of the reads ONLY to the forward strand of the provided reference?
Targeted RNA-seq Rhapsody BD
updated 4.2 years ago by 154k • written 4.2 years ago by • 0
1
vote
3
replies
2.7k
views
GO and KEGG pathway analysis of lncRNA genes
GO lncRNA clusterProfiler KEGG pathway
updated 4.2 years ago by ★ 2.6k • written 4.7 years ago by ▴ 140
1
vote
1
reply
1.6k
views
clusterProfiler gene list retrieval
clusterProfiler GO KEGG Reactome ontology
updated 4.2 years ago by ★ 2.6k • written 4.9 years ago by ▴ 30
0
votes
1
reply
941
views
Determine where an interleaved FASTQ record starts
fastq
updated 4.2 years ago by 21k • written 4.2 years ago by ★ 4.5k
1
vote
3
replies
1.7k
views
How to compare alignments(SAM/BAM files) aligned to different references?
sam WGS NGS bam alignment
updated 4.2 years ago by ▴ 600 • written 4.2 years ago by ▴ 20
3
votes
4
replies
2.8k
views
Aligning 23andme to reference genome
alignment txt 23andme
4.2 years ago by Manuel • 0
0
votes
3
replies
4.1k
views
Forum: How to calculate LDDT score for protein structure ?
LDDT PBD
updated 3.9 years ago by • 0 • written 4.2 years ago by • 0
2
votes
5
replies
3.2k
views
Bioperl SeqIO.pm cannot be found
feelnc lncRNA bioperl
4.1 years ago by bart ▴ 50
0
votes
1
reply
2.7k
views
Creating Signature Matrix from SC-RNA Seq data for Deconvolution of Bulk Tissue
deconvolution rna-seq cibersort
updated 4.2 years ago by ▴ 250 • written 4.2 years ago by ▴ 10
1
vote
1
reply
1.2k
views
Normalizing 5' Nascent RNA-seq data to identify differentially expressed transcription start sites
Deseq2 vst rle transformation
updated 4.2 years ago by 89k • written 4.2 years ago by ▴ 10
2
votes
7
replies
2.4k
views
Allele-Specific analysis for human WGBS data
allele methylation WGBS allelespecific dna
4.2 years ago by Ankit ▴ 520
4
votes
3
replies
1.6k
views
somatic short variant calling from patients having autoimmune disease
somatic immunedisease gatk variant
4.2 years ago by Mehmet ▴ 820
4
votes
9
replies
2.4k
views
Merge files in Plink
Plink
updated 4.2 years ago by 11k • written 4.2 years ago by ▴ 10
2
votes
2
replies
2.1k
views
GEO submission when I have raw data in SRA
GEO SRA scRNA-seq NCBI data
updated 4.2 years ago by 9.0k • written 4.2 years ago by ▴ 90
0
votes
0
replies
540
views
How to get good mapping for miRNA-seq data by removing rRNA/tRNA
miRNA
4.2 years ago by Ss.sharifi2015 ▴ 20
3
votes
5
replies
5.3k
views
BUSCO installation and run
RNAseq
updated 4.2 years ago by 8.9k • written 4.2 years ago by ▴ 480
0
votes
0
replies
675
views
how to plot genetic struture of bacterial genes?
bacteria plot gene
updated 4.2 years ago by 45k • written 4.2 years ago by ▴ 110
0
votes
0
replies
727
views
Karyotyping variation by ethnicity
structural SV ethnicity variation karyotype
4.2 years ago by gnmcsbnfrmtcsclb ▴ 70
0
votes
2
replies
2.7k
views
Linux command to delete empty fastq.gz files
linux fastq gz
updated 4.2 years ago by 21k • written 4.2 years ago by • 0
0
votes
0
replies
1.1k
views
VCF to 23 and Me format and changing ensamble reference help needed for underestanding VCF
23andMe VCF
4.2 years ago by aliciabasilo.ab • 0
0
votes
0
replies
831
views
Download COG Database
database COG
4.2 years ago by gaurav.iari • 0
3
votes
2
replies
2.0k
views
How to interpret bimodal distribution of GC-content for RNAseq and can it be remedied ?
RNA-Seq GCcontent FastQC RNAseq
updated 4.2 years ago by 154k • written 4.2 years ago by ▴ 220
5
votes
3
replies
2.3k
views
AnnotationHub::mapIds() cannot find existing ENSG (GEO supplemental data cross-referenced with ensembl.org)
ensg annotationhub mapping
4.2 years ago by mk ▴ 310
1
vote
5
replies
2.3k
views
De novo genome assembly
De novo Assembly Genome Minimap2 Mother
updated 4.2 years ago by 154k • written 4.2 years ago by • 0
1
vote
0
replies
1.2k
views
hisat2 compatibility for long read
Long-read hisat2
updated 2.3 years ago by 45k • written 4.2 years ago by ▴ 20
2
votes
1
reply
3.3k
views
illumina adapter specifying and removing using fastp
adapter index illumina fastp fastq
updated 4.2 years ago by 154k • written 4.2 years ago by ▴ 820
0
votes
2
replies
1.3k
views
Extremely low number of variants in VCF file after filtering MIN(FORMAT/DP)>10
bcftools snp vcf calling
updated 4.2 years ago by 21k • written 4.2 years ago by ▴ 80
0
votes
1
reply
2.1k
views
extract list of SNPs from multiple chr{1:22}.bgen files using plink2
subset of extract maf SNPs cutoff plink2
updated 4.2 years ago by 11k • written 4.2 years ago by ▴ 10
122,013 results • Page 600 of 2441
Recent Votes
Answer: 1 vs 1 DEG analysis in scrna seq data
Comment: installation of package ‘DESeq2’ had non-zero exit status
Answer: Recommendations for 200 SNP markers genotyping
Comment: Reasonable number of SNPs in a bacterial genome.
The Biostar Handbook. A bioinformatics e-book for beginners.
Genome Assembly QC from BAM files
Answer: Scaling RNA-Seq data before clustering?
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Popular Question to firestar ★ 1.7k
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Answer: 1 vs 1 DEG analysis in scrna seq data by ATpoint 89k
The only option you have is to treat every single cell as a replicate. That has the obvious downside that any effect can be a donor-unique …
Answer: GUI commercial software for 10x single cell gene expression analysis by firestar ★ 1.7k
An open-source option: [kana](https://www.kanaverse.org/kana/).
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Edward • 0
Yes, we plan to make English the primary language of the Brave UI.
Comment: Reasonable number of SNPs in a bacterial genome. by michael.ante ★ 4.0k
If your bacterial species is a (human) pathogen, you might want to check outbreak analysis papers of that species. In general, you find t…
Comment: hisat2 error-Paired end reads not equal or lack of RAM/disk space? by lieven.sterck 16k
ok, missed that ... in any case that should not happen indeed. How did you determine that the files are not equal? I can indeed also see t…
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Ram 45k
Do you have a plan to make an English version of the UI?
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Edward • 0
This can visualize the parameters of the generated workflow, software, and scripts, and manage the docker process of the script, software, …
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by ATpoint 89k
Can you summarize in one sentence what the use case is? Is this a workflow manager?
Comment: Pseudogene - scarce info by ATpoint 89k
This reminds me strongly on my "masters" courses (doesn't deserve that name tbf). "Here is some poorly-described project with little to no …
Answer: scVI vs Harmony, which is better for cell type based clustering in brain tissue? by ATpoint 89k
There is no "better" is my experience. It always depends on the dataset. Try both and integrate your biological knowledge to decide which m…
Comment: DESeq2 on metagenome KO counts by Aleksandra ▴ 190
I just wrote that I misunderstood your initial question.
Comment: DESeq2 on metagenome KO counts by Aleksandra ▴ 190
What exactly did I not get?
Comment: Interpreting genomic features distribution for CUT&RUN peaks by rfran010 ★ 1.7k
If I understand correctly, you see increased signal at TSS sites compared to control (taller peaks in browser). However, 92% of the 450 siS…
Comment: combine VCF from diploid reference/haplotypes for the same sample by cmdcolin ★ 4.3k
this question is a little similar to your previous question (https://www.biostars.org/p/9614638/). just as added info, here is a tool calle…
Comment: hisat2 error-Paired end reads not equal or lack of RAM/disk space? by aj123 ▴ 130
As mentioned above, I just got the raw fastq files from the ftp site listed.
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