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add text to a path by adding text to it with python (FTP Path NCBI)
python ncbi pandas
4.3 years ago by Debut ▴ 20
1
vote
0
replies
907
views
Job: Opportunity: Bioinformatics Software Engineer - Bioinformatics Core @ Memorial Sloan Kettering Cancer Center, New York, NY (US)
cancer_biology Python R
updated 4.3 years ago by 45k • written 4.3 years ago by ▴ 10
0
votes
1
reply
806
views
Differential Expression Analysis Using RPKM
RPKM RNA-seq DE
updated 4.3 years ago by 15k • written 4.3 years ago by • 0
1
vote
1
reply
1.0k
views
Single cell clusters annotating to same cell-type
Monocle Single-cell Seurat Pseudotime
updated 4.3 years ago by ★ 1.1k • written 4.3 years ago by ▴ 50
0
votes
2
replies
1.2k
views
Exact duplicated reads between independent replicates
ChIP NGS low-input duplicates Illumina
4.3 years ago by Miguel • 0
0
votes
1
reply
1.9k
views
Surat object UMAP - highlight cells based on Citeseq data
Seurat UMAP
updated 4.3 years ago by 3.4k • written 4.3 years ago by ▴ 40
2
votes
1
reply
1.0k
views
Obtaining all independent SNPs
SNPs permutation pruning clumping PLINK
updated 4.3 years ago by ★ 4.8k • written 4.3 years ago by ▴ 10
1
vote
2
replies
1.2k
views
Cytoscape for co-occurence network analysis
Microbiome 16S analysis Cytoscape Network
4.3 years ago by Bioinfonext ▴ 480
3
votes
2
replies
2.2k
views
Structural variants calling in a population
structural variants
updated 4.3 years ago by • 0 • written 8.3 years ago by ★ 1.0k
5
votes
4
replies
7.3k
views
Merge vcf files of structural variants
structural_variants vcf merge
updated 4.3 years ago by • 0 • written 7.1 years ago by ▴ 20
3
votes
2
replies
4.2k
views
For loop to parallel run commands
Unix bash Linux
4.3 years ago by endretoth ▴ 40
19
votes
13
replies
9.8k
views
8 follow
Error installing bcl2fastq 2.20 in make step - Ubuntu 18.04
software error bcl2fastq ubuntu
updated 2.8 years ago by • 0 • written 6.3 years ago by ▴ 140
0
votes
2
replies
810
views
Pseudogenes identification and removal from BRCA samples
NGS
4.3 years ago by smrutimayipanda ▴ 20
0
votes
3
replies
1.0k
views
very low number of reads aligned in bowtie (colourspace)
map colourspace bowtie
updated 4.3 years ago by 154k • written 4.3 years ago by ★ 1.3k
1
vote
1
reply
806
views
Multiple genes comparison
Transcriptome RNA-seq
updated 4.3 years ago by ▴ 160 • written 4.3 years ago by ▴ 10
0
votes
2
replies
1.3k
views
Tools for SNPs and Indels (RNA seq. Nanopore)
Indel RNA-Seq SNP Nanopore
updated 2.6 years ago by 45k • written 4.3 years ago by ▴ 30
4
votes
3
replies
1.9k
views
Complex DESeq2 sample file set up
complex design DESEq2 RNAseq
4.3 years ago by rva_jango ▴ 10
0
votes
0
replies
843
views
Job: Bioinformatician at the Institute of Botany, Czech Academy of Sciences
polyploidization diversification plant
updated 4.3 years ago by 45k • written 4.3 years ago by • 0
0
votes
3
replies
1.3k
views
DESeq2: Variable Importance
DESeq2
updated 4.3 years ago by 89k • written 4.3 years ago by ▴ 30
1
vote
6
replies
2.1k
views
Is BLASTp the quickest method to get a rough idea on ortholog from protein sequence?
blastp ortholog homolog blast
updated 4.3 years ago by 16k • written 4.3 years ago by ▴ 190
0
votes
0
replies
539
views
GOstat error : No results met the specified criteria
RNAseq GO gostat
4.3 years ago by ryme ▴ 30
4
votes
2
replies
1.1k
views
Remote access- data security
Remote-Access
updated 4.3 years ago by ★ 3.4k • written 4.3 years ago by ▴ 110
1
vote
1
reply
1.4k
views
Imputation with Beagle 5.2 for whole exome data at once
Beagle Imputation
updated 4.3 years ago by 2.9k • written 4.3 years ago by ▴ 10
0
votes
2
replies
1.5k
views
Pedigree file for 1k genome , build 38
build 1000G pca 38
4.3 years ago by AVA ▴ 40
5
votes
3
replies
1.5k
views
Why is NNN sequence at the end of chromosomes
Telomere sequence NNN
4.3 years ago by cammm988 ▴ 10
1
vote
1
reply
1.1k
views
How to calculate the *necessary* sequencing depth for a SNP
sequencing SNP analysis depth statistics Sequencing
updated 4.3 years ago by ▴ 730 • written 4.3 years ago by • 0
0
votes
1
reply
802
views
Change genbank files orientation to '5 > '3 based on their ORF direction
reverse genbank ORF complete
updated 4.3 years ago by 22k • written 4.3 years ago by ▴ 10
3
votes
9
replies
2.4k
views
Alternative polyadenylation detection from short-read RNA-seq, software suggestions
software apa alternative-polyadenylation
4.3 years ago by Gregor Rot ▴ 550
2
votes
4
replies
2.3k
views
KRAKEN2 database build ref-seq have some missing data
KRAKEN2 ref-seq
4.3 years ago by jimmy0958073736 ▴ 40
1
vote
4
replies
1.1k
views
How to verify the authenticity of the data set downloaded from database?
data analysis
4.3 years ago by 465336766 • 0
1
vote
6
replies
4.3k
views
bcftools plugin fill-tags with functions
AVG fill-tags bcftools
4.3 years ago by diana.cornejo • 0
3
votes
4
replies
1.9k
views
Duplicate results in vardict vcf
vardict
updated 4.3 years ago by 45k • written 4.3 years ago by ▴ 60
6
votes
4
replies
2.9k
views
Unable to install EnhancedVolcano: non-zero exit status
Harfbuzz EnhancedVolcano R
updated 4.3 years ago by 89k • written 4.3 years ago by ▴ 90
1
vote
2
replies
1.2k
views
How can I format blastn output?
blast pairwise blastn alignment
updated 4.3 years ago by 154k • written 4.3 years ago by • 0
1
vote
4
replies
1.6k
views
PopGenome Not Reading In FASTA File
popgenome MKT selection R phylogenomics
4.3 years ago by Simone ▴ 10
0
votes
1
reply
1.8k
views
error in anvi'o tool
python software error genome R gene
updated 4.3 years ago by • 0 • written 4.6 years ago by ▴ 120
4
votes
1
reply
742
views
Does anyone know if there is an implementation of overlaping kmeans algorithm in R ?
r partitional-clustering kmeans
updated 4.3 years ago by ★ 30k • written 4.3 years ago by ▴ 140
0
votes
2
replies
1.5k
views
How to combine UMIs split across reads 1 and 2 into a single UMI for deduplication?
umitools umi
4.3 years ago by SethG • 0
0
votes
0
replies
898
views
Job: Bioinformatics Job Opening
genomics RNA
updated 4.3 years ago by 45k • written 4.3 years ago by ▴ 110
0
votes
0
replies
537
views
Job: senior bioinformatician, University of Cambridge (UK) - 3years contract
three_years_contract Senior_bioinformatician
4.3 years ago by davide.chiarugi ▴ 20
4
votes
5
replies
15k
views
Extract rows name in R
rows R
updated 4.3 years ago by 12k • written 4.3 years ago by ▴ 30
0
votes
1
reply
1.1k
views
How two merge two different interactome networks?
Network analysis Network merge
updated 4.3 years ago by ▴ 70 • written 4.6 years ago by • 0
1
vote
2
replies
1.2k
views
Download MuSiC RNAseq analysis program
devtools MuSiC RNAseq
4.3 years ago by - • 0
0
votes
0
replies
653
views
Job: Postdoctoral Associate - 121648
DHVI Duke Postdoc
updated 4.3 years ago by 45k • written 4.3 years ago by • 0
0
votes
0
replies
956
views
Artic protocol
variant-calling artic nanopre sars-cov-2 medaka
4.3 years ago by juanjo75es ▴ 130
2
votes
3
replies
2.1k
views
How to change my SNP Id format from chr1_847228_C_T to chr1_847228 in my .bim file.
Chromosome SNP position Plink unix rsid
updated 4.3 years ago by ★ 4.8k • written 4.3 years ago by ▴ 20
1
vote
3
replies
1.9k
views
PGS Catalog file does not have rsID
Catalog CAD PGS PRSice
updated 4.0 years ago by ★ 4.8k • written 4.3 years ago by ▴ 20
0
votes
0
replies
509
views
I see SNP in IGB but not in my .vcf file
mapping snp
updated 4.3 years ago by 45k • written 4.3 years ago by • 0
5
votes
2
replies
1.7k
views
Kallisto alignment method for single nuclei
Kallisto
updated 4.3 years ago by ★ 7.7k • written 4.3 years ago by ▴ 20
3
votes
8
replies
6.9k
views
Plink update name flag, setting column names
plink update-name
updated 4.3 years ago by 12k • written 4.4 years ago by ▴ 70
121,983 results • Page 636 of 2440
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Is this an appropriate command for estimating contaminatin in a germline WGS sample using GATK?
Answer: Dorado in PowerShell on Windows
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Answer: When to merge RNA-seq files with multiple sequencing lanes
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Recent Replies
Answer: Corresponding BAM files by GenoMax 154k
You can get BAM files for 10x single-cell data and they can be found under the `Data Access` tab of the SRA record under the `Original Form…
Comment: GTF file for HIV strain pNL4-3 by Ales ▴ 50
All of the genome assemblies are from the LANL compendiu, match accession with GENBANK (>2,000 complete genome assemblies from the 2021 LAN…
Comment: Hisat2 splice sites extract blank files by Ales ▴ 50
hisat2_extract...py scripts make several assumptions about the input GTF files. For example, they require gene_id field to be present for a…
Comment: GTF file for HIV strain pNL4-3 by GenoMax 154k
> This project started from my personal need to improve spliced alignment Are there plans to submit these annotations to NCBI/EBI? Are yo…
Comment: Hisat2 splice sites extract blank files by Ales ▴ 50
Interestingly, HIV/SIV specifically does have quite an elaborate splicing system which regulates translation. However, only one of the spli…
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I'm late to the party but in case someone has the same question: one practical approach is using **rank-based** methods to meta-analyse you…
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I'm late to the party but one practical approach is using **rank-based** methods to meta-analyse your screens, which basically bypass the n…
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Should be noted that the gtf/gff and genomic.fna files for HIV only contain CDS annotations of the 9 ORFs and not the full transcripts. Onl…
Comment: GTF file for HIV strain pNL4-3 by Ales ▴ 50
just wanted to follow up that to address this specific issue we just released HIV transcriptome annotations of alternative splicing featuri…
Answer: GTF file for HIV strain pNL4-3 by Ales ▴ 50
For anyone stumbling on this. We have recently completed reference-grade annotation for several thousand HIV-1 genomes including the HXB2 (…
Comment: Dorado in PowerShell on Windows by sbissi102 ▴ 10
Yes, I found all the barcodes, but could working on WSL affect the basecalling results?
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Since I was running in stub-run mode, the solution was to make unique names for the FASTQC process like this: touch ${sample}_${rea…
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Many researchers use the CLC Genomics Workbench and Ingenuity Pathway Analysis. CLC can be used to do secondary analysis for your dataset a…
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For example, in this image, the red area represents the differentially acetylated region returned by DiffBind. The green area is a promoter…
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Interesting pricing model : https://www.nygen.io/pricing Depending on user needs could be used (or certainly tested) for free. And this is …
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