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795 results • Page 3 of 16
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4
votes
9
replies
2.3k
views
How to view bigwig files in UCSC with windowed coverage?
ucsc atac-seq ChIP-Seq
updated 1 hour ago by 39k • written 3.5 years ago by ▴ 200
4
votes
13
replies
471
views
Limma returned only positive logFC values
edgeR differential-expression deg limma
updated 5 hours ago by 72k • written 1 day ago by ▴ 40
4
votes
12
replies
1.2k
views
Forum: publicly available data
arrayexpress GEO SRA
updated 2 days ago by 39k • written 3.7 years ago by ▴ 110
4
votes
3
replies
5.4k
views
ATACseq alignment issues
BWA alignment ATAC-seq
updated 1 hour ago by 39k • written 7.5 years ago by • 0
4
votes
11
replies
1.8k
views
6 follow
The fastest protein sequence aligner available
protein sequence alignment
updated 6 days ago by ▴ 70 • written 5.0 years ago by ▴ 360
4
votes
0
replies
1.2k
views
Job: Ensembl Outreach Officer
training ensembl
updated 6 days ago by 39k • written 4.0 years ago by 23k
4
votes
12
replies
840
views
Separating text from one column in R
R
updated 6 days ago by 39k • written 4.0 years ago by • 0
4
votes
6
replies
2.4k
views
Forum: NGS Data Storage Best Practices (Clinical)
NGS clinical storage
updated 1 day ago by 39k • written 3.5 years ago by ▴ 630
4
votes
4
replies
1.6k
views
how to identify disease variants from bam file ?
disease-variants VCF bam ATAC-seq
updated 1 hour ago by 39k • written 4.5 years ago by ▴ 20
4
votes
2
replies
1.1k
views
News: Hands-On Workshop: How to use bisulfite-treated sequencing to study DNA methylation (BS-Seq, Bisulfite-Seq, WGBS)
Workshop methylation bisulfite
updated 2 days ago by 39k • written 3.7 years ago by ▴ 970
4
votes
0
replies
915
views
Forum: Plotting Ensembl gene name changes between versions
R ensembl
updated 5 days ago by 39k • written 3.8 years ago by ▴ 550
4
votes
7
replies
5.2k
views
Help making ADMIXTURE output digestible
admixture
updated 6 days ago by ▴ 20 • written 7.8 years ago by ▴ 730
4
votes
0
replies
1.4k
views
Job: PhD studentship in bioinformatics: Network Inference and Systems Biology
network-biology
updated 3 hours ago by 39k • written 3.4 years ago by ▴ 40
3
votes
0
replies
595
views
News: Testing and feedback of upcoming salmon release
salmon RNA-Seq
updated 4 days ago by 39k • written 3.7 years ago by 6.1k
3
votes
4
replies
273
views
Gene prediction software
pseudogene gene prediction masking
updated 9 hours ago by 4.4k • written 1 day ago by ▴ 20
3
votes
0
replies
1.4k
views
Job: American Museum of Natural History - Bioinformatics Specialist
genomics
updated 4 days ago by 39k • written 3.8 years ago by ▴ 30
3
votes
12
replies
2.2k
views
What is NCBI Gene ID, where to find it and how to convert to entrez ID?
RNA-Seq
updated 5 days ago by ▴ 90 • written 3.7 years ago by ▴ 10
3
votes
1
reply
1.4k
views
Performing Hmmer search against pfam versus UniRef100
hmmer pfam alignment
updated 4 days ago by 39k • written 3.8 years ago by • 0
3
votes
3
replies
336
views
Perl. How to retrieve data until a keyword in GenBank?
fasta sequence GenBank perl
1 day ago by Fungi-Beware! ▴ 10
3
votes
0
replies
676
views
News: Phylogenomics course in Berlin
snp R next-gen
updated 1 day ago by 39k • written 3.5 years ago by ★ 2.3k
3
votes
5
replies
439
views
RNASeq gene labeling and mRNA filter from bulkRNA data.
RNA-Seq RSubreads
updated 1 day ago by ▴ 160 • written 5 days ago by • 0
3
votes
0
replies
881
views
Forum: Good books on application of Machine Learning in Bioinformatics
book machine-learning
updated 4 days ago by 39k • written 3.8 years ago by ▴ 180
3
votes
3
replies
351
views
Retrieving allele-specific information for a variant using VEP annotation
variant-calling VEP COSMIC
5 days ago by bt_cepo ▴ 20
3
votes
0
replies
658
views
News: ::FINAL CALL:: NGS Data Analysis for Beginners - 11-13 December 2019 in Munich, Germany (2 seats left)
NGS Workshop
updated 1 day ago by 39k • written 3.6 years ago by 9.9k
3
votes
3
replies
1.3k
views
Bridge Amplification error rate and duplicates in NGS
NGS PCR-duplicates bridge-pcr next-gen
updated 5 days ago by 39k • written 3.9 years ago by ▴ 20
3
votes
4
replies
220
views
retaining only the clusters of interest
seurat single-cell scRna-seq
updated 4 hours ago by 39k • written 22 hours ago by • 0
3
votes
1
reply
731
views
Job: Bioinformatician in personalized oncotherapy (BEL)
next-gen-sequencing genome SNP
updated 1 day ago by 39k • written 3.5 years ago by ▴ 20
3
votes
0
replies
1.3k
views
News: Analysis of single cell RNA-seq data - Berlin 23 -27 March 2020
scRNA-seq RNA-Seq
updated 6 days ago by 39k • written 3.9 years ago by ★ 2.3k
3
votes
7
replies
1.1k
views
Find 3'UTRs for species
Assembly alignment
updated 4 days ago by 39k • written 3.8 years ago by ▴ 110
3
votes
3
replies
905
views
Forum: Large Multi-omics Project -- Dev Approach
snp RNA-Seq sequencing
updated 4 days ago by 39k • written 3.8 years ago by ▴ 10
3
votes
3
replies
319
views
Why is coordinate sort required before findng read depths?
wgs sambamba
updated 2 days ago by ▴ 10 • written 4 days ago by • 0
3
votes
4
replies
298
views
bcftools "--filter-logic" flag, what + means?
bcftools vcf
updated 2 days ago by ▴ 360 • written 5 days ago by ▴ 170
3
votes
3
replies
246
views
Gene enrichment analysis
Go enrichment r gene
updated 2 days ago by 130k • written 2 days ago by • 0
3
votes
2
replies
1.1k
views
Binding matrix created by DiffBind
DiffBind atac-seq dba
updated 1 hour ago by 39k • written 24 months ago by ▴ 10
3
votes
7
replies
442
views
How to sort gff3 according to chromosome order?
gff3 sort
updated 4 days ago by 154k • written 4 days ago by • 0
3
votes
7
replies
4.2k
views
Getting Pairwise Sequence Alignment Score With Biopython
biopython alignment clustalw
updated 1 day ago by ▴ 70 • written 11.5 years ago by • 0
3
votes
2
replies
881
views
Creating a genotype matrix for BeviMed
snp genome Bayesian
updated 2 hours ago by 39k • written 3.4 years ago by ▴ 110
3
votes
1
reply
687
views
News: PrecisionFDA has won a FedHealth IT award!!
platform cloud-based precision-medicine award
updated 6 days ago by 39k • written 4.0 years ago by ▴ 150
3
votes
2
replies
149
views
Panther db Reference List
pantherdb enrichment-tests
updated 6 days ago by 39k • written 7 days ago by ▴ 50
3
votes
9
replies
679
views
Get protein information from ensemblbacteria using interpro
ensembl
updated 1 day ago by ▴ 10 • written 22 days ago by • 0
3
votes
6
replies
2.0k
views
h5ad cellxgene to R
single-cell h5 cellxgene anndata R
updated 3 days ago by 130k • written 6 months ago by ★ 1.5k
3
votes
0
replies
968
views
Job: Three PI positions in neurogenomics or neuroscience at VIB-UAntwerp (Belgium)
VIB neuroscience genomics
updated 2 days ago by 39k • written 3.7 years ago by 47k
3
votes
2
replies
899
views
Job: Postdoc in computational and experimental annotation of tRNA-related sequences
qPCR plant hybridization genomics trna
updated 4 days ago by 39k • written 3.7 years ago by 11k
3
votes
3
replies
1.4k
views
Error in installation of RandFold 2.0
Linux rna-seq Ubuntu
updated 2 days ago by 39k • written 3.7 years ago by ▴ 30
3
votes
0
replies
1.1k
views
News: Nextflow Training Course
Pipeline Workflow NEXTFLOW
updated 2 days ago by 39k • written 3.7 years ago by ★ 2.3k
3
votes
8
replies
2.7k
views
6 follow
Forum: SSD or HHD for genome analysis
hardware genome sequencing
updated 2 days ago by 39k • written 3.7 years ago by ▴ 10
3
votes
4
replies
1.3k
views
Job: GSK Data Strategy & Design Expert
NGS DATA R GSK
updated 2 hours ago by 39k • written 3.3 years ago by ▴ 40
3
votes
3
replies
2.9k
views
Normalize BigWig's for # of reads in peaks and sequencing depth
Deeptools ATAC-seq
updated 1 hour ago by 39k • written 3.3 years ago by • 0
3
votes
5
replies
2.1k
views
STAR genome generate taking long time and less thread.
RNA-Seq STAR
updated 5 days ago by 39k • written 3.8 years ago by ▴ 70
3
votes
5
replies
1.8k
views
should non-protein-coding rna(e.g. lncRNA) be removed in RNA-Seq differential expression analysis
RNA-Seq rna-seq
updated 2 days ago by ▴ 80 • written 4.2 years ago by ▴ 40
795 results • Page 3 of 16
Recent Votes
Comment: Saving results from yeastgenome.org blastp search
Comment: snps from empty well, Illumina Sequencing
Extract sequences from a fastq file by a list of IDs
Answer: Extract sequences from a fastq file by a list of IDs
Answer: Differences in GTF files hg19 and hg38
Answer: CHiP-Seq Questions
Answer: Diff Bind Questions
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Recent Replies
Comment: Saving results from yeastgenome.org blastp search by GenoMax 130k
Unless yeastgenome site provides a way to do that, you likely can't. Do the search over at NCBI (limit search by using taxonomy to mimic wh…
Answer: Differences in GTF files hg19 and hg38 by GenoMax 130k
Not sure where you got your GTF for GRCh38 from but [**one from GENCODE**][1] has the level info you are looking for. chr1 HAVANA…
Comment: CHiP-Seq Questions by B.N. • 0
Thank you for the suggestions Dr. Stark.
Comment: Diff Bind Questions by B.N. • 0
Thank you so much for the insight Dr. Stark!
Comment: Is PanCan data microarray or rna-seq by GenoMax 130k
This particular example ("GeneChip") is an array. Early TCGA samples may have been done using arrays and later sequenced. Appears to be thi…
Comment: ChatGPT optimized for bioinformatics questions by Sasha ▴ 280
Hoping to add functionality around this. Stay tuned. Big problem for our space that needs to be resolved.
Comment: Is PanCan data microarray or rna-seq by solarchan7 • 0
Hi, so this [paper](https://www.nature.com/articles/s41598-019-45165-4) uses the TCGA dataset and in the supplementary information, it ment…
Comment: counts matrix should be numeric, currently it has mode: character when using a c by Darked89 4.4k
Since the input file is named `normalized.csv` and the values look like floats most likely the counts have been already normalized somehow.
Comment: Embryo transcriptome by Basti ★ 1.6k
https://www.ebi.ac.uk/ena/browser/view/PRJEB11202 https://www.ebi.ac.uk/ena/browser/view/PRJNA153427
Comment: ChatGPT optimized for bioinformatics questions by ATpoint 72k
How is it trained on PubMed/papers? One major drawback of ChatGPT is that it wildly makes up papers that do not even exist but with great c…
Answer: sgRNA design by ATpoint 72k
gRNAs are single-stranded and by this they have a strand-specificity (depends where the PAM is) and that gives them an orientation.
Answer: counts matrix should be numeric, currently it has mode: character when using a c by ATpoint 72k
You have commas as decimal delimiters which interpreted as text. Just replace by dot and make numeric: ```r d <- data.frame(A=c("1,2", "3,…
Comment: snps from empty well, Illumina Sequencing by GenoMax 130k
> I receive illumina sequencing files with 96 wells, our lab leaves one > well empty. When I process the files with a SNP calling pipeline …
Answer: counts matrix should be numeric, currently it has mode: character when using a c by Darked89 4.4k
You can try: counts_data <- read.csv2("normalized.csv", header = TRUE) But as far as I know DESeq2 requires raw counts as inpu…
Comment: Is there bioinformatics tool to check cross hybridization between primers and pr by Tawny ▴ 180
Was a tool ever found for this? I am curious.
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