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121,983 results • Page 642 of 2440
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2
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3
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1.3k
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plotting stacked bar plot with different number and kinds of variables
stackedbarplot ggplot
4.4 years ago by Curls ▴ 40
1
vote
6
replies
3.2k
views
how to implement a database with several FASTA files
Database NCBI FASTA
updated 4.4 years ago by 103k • written 4.4 years ago by ▴ 20
1
vote
3
replies
2.6k
views
PAM250 and BLOSUM62 probability of substitution matrices
blosum matrix pam
updated 4.4 years ago by ★ 30k • written 4.4 years ago by • 0
0
votes
0
replies
731
views
Goseq - Pwf: Error In If (Hi <= Low) { : Missing Value Where True/False Needed
r goseq ontology Gene GO
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 30
0
votes
0
replies
659
views
How to derive an inverse simpson index(alpha diversity) from the phylosift results
phylosift alpha diversity
4.4 years ago by tmfdk0819 • 0
0
votes
2
replies
1.2k
views
Clustering artefacts when processing single-nucleus RNAseq
single-cell RNA Seurat UMAP
4.4 years ago by MikeV ▴ 10
4
votes
8
replies
9.1k
views
Help with designing limma contrast matrix
limma software error
updated 2.6 years ago by 89k • written 7.6 years ago by ★ 4.4k
1
vote
4
replies
2.8k
views
deeptools 3.5 plotCorrelation
ChIP-Seq sequencing plotCorrelation next-gen deeptools
updated 4.4 years ago by 9.0k • written 4.4 years ago by ▴ 20
4
votes
11
replies
11k
views
7 follow
Single cell DEG analysis. Wildly different results from different FindMarkers test
rna-seq seurat
updated 4.4 years ago by 45k • written 5.1 years ago by ▴ 20
0
votes
5
replies
2.1k
views
TCGA data Query (GDCquery): external_gene_name " are missing
TCGABiolinks R TCGA
updated 2.5 years ago by 45k • written 4.4 years ago by • 0
7
votes
1
reply
1.4k
views
Herald: The Biostar Herald for Wednesday, June 02, 2021
herald
updated 4.4 years ago by 103k • written 4.4 years ago by 3.6k
10
votes
11
replies
5.9k
views
Help with rownames in DESeq2
DESeq2 DEG Rstudio R
updated 4.4 years ago by • 0 • written 4.4 years ago by ▴ 10
0
votes
0
replies
786
views
News: Event: Women in data science and bioinformatics - perspectives from industry and academia
gender women equality event data-science
updated 4.3 years ago by 45k • written 4.4 years ago by ▴ 470
4
votes
2
replies
1.6k
views
Use TPM to compare between the samples
TPM Analysis RNA-seq DE
4.4 years ago by Kunal • 0
1
vote
5
replies
3.8k
views
SNPs file for reference genome (Mouse - GRCm39)
Mouse SNPs Rna-seq Genome GRCm39
4.3 years ago by David Martínez ▴ 10
1
vote
10
replies
3.0k
views
Help with mitochondrial sequences from GenBank!!!
ftp genbank mitochondrial
4.4 years ago by Matteo Ungaro ▴ 130
0
votes
0
replies
921
views
Job: ELIXIR/EMBL-EBI: Front-end or full-stack web developer
front-end web-developer data FAIR
updated 4.3 years ago by 45k • written 4.4 years ago by ▴ 470
0
votes
0
replies
1.0k
views
Job: ELIXIR/EMBL-EBI: Project Manager/Senior Project Coordinator - COVID-19
EMBL-EBI project data COVID-19 COVID management
4.4 years ago by Erin Haskell ▴ 470
0
votes
4
replies
1.3k
views
Mutation Software
Mutation
updated 4.3 years ago by 89k • written 4.4 years ago by • 0
0
votes
1
reply
829
views
RNA-seq: extraction and annotation of differentially expressed genes
RNAseq Galaxy DEG analysis
updated 4.4 years ago by 9.0k • written 4.4 years ago by ▴ 10
8
votes
8
replies
3.2k
views
Do I need Illumina Demultiplexing for RNASeq?
Demultiplexing Galaxy RNASeq
updated 4.3 years ago by 154k • written 4.4 years ago by ▴ 20
2
votes
1
reply
2.5k
views
Creating a haplotype map now that the HapMap site has been taken down
HapMap
updated 4.4 years ago by • 0 • written 9.2 years ago by ▴ 10
5
votes
10
replies
6.3k
views
9 follow
Error ecountered while running conifer with demo data set
conifer python numpy cnv
updated 4.4 years ago by ▴ 20 • written 8.2 years ago by ▴ 10
2
votes
1
reply
912
views
STRINGdb "Expected Interactions"?
STRINGdb
updated 4.4 years ago by ★ 30k • written 4.4 years ago by ▴ 30
4
votes
4
replies
2.5k
views
How much weights a million reads
sequencing
4.4 years ago by gubrins ▴ 350
0
votes
4
replies
1.1k
views
Gene-filterin In R
R
4.3 years ago by soniabedi.07 ▴ 30
4
votes
3
replies
3.1k
views
STAR Aligner --quantMode GeneCounts
RNA-Seq STAR
updated 4.4 years ago by 15k • written 4.4 years ago by ▴ 80
2
votes
2
replies
4.0k
views
Extract chromosome 1 - 22 ,X and Y from BAM file
NGS
updated 4.4 years ago by 14k • written 4.4 years ago by ▴ 40
0
votes
0
replies
639
views
Haplotype inference algorithms in Pedigrees
algorithms pedigree inference snps haplotype
4.4 years ago by S. Roa ▴ 10
2
votes
1
reply
1.5k
views
What does “non-log-linear space” mean for genomic data?
Data
updated 4.4 years ago by 11k • written 4.4 years ago by ▴ 10
0
votes
4
replies
2.0k
views
ComplexHeatmap Package takes forever to plot
ComplexHeatmap heatmap
updated 4.4 years ago by 21k • written 4.4 years ago by • 0
0
votes
0
replies
619
views
Differentiating alleles from paralogs in comparison of transcriptomes within species
clustering transcriptome paralog trinity assembly
4.3 years ago by jfaberha ▴ 50
2
votes
2
replies
982
views
Concatenate multifastas
join fasta concatenate multifasta
4.4 years ago by Colaptes ▴ 120
0
votes
2
replies
2.8k
views
TCGA-BRCA downloading issue by GDCquery
TCGABiolinks TCGA-BRCA
updated 2.5 years ago by 45k • written 4.4 years ago by • 0
2
votes
3
replies
2.8k
views
merging two VCF files
gatk dictionary vcf
updated 4.4 years ago by ▴ 480 • written 4.4 years ago by ▴ 110
0
votes
0
replies
523
views
Tools to view pacbio assembly
genome
4.4 years ago by K ▴ 10
1
vote
4
replies
5.4k
views
Reasons For Low Ts/Tv Ratio
exome snp
written 14.0 years ago by ▴ 110
2
votes
1
reply
1.9k
views
gffcompare class_code "u"
gffcompare
updated 4.4 years ago by ▴ 290 • written 4.4 years ago by • 0
0
votes
4
replies
3.1k
views
Low Counts with featureCounts
RNA-Seq featureCounts
updated 4.4 years ago by ▴ 290 • written 5.2 years ago by • 0
2
votes
3
replies
2.1k
views
How we can use DEG data for GSEA analysis
GSEA
4.4 years ago by yeshiwork2000 • 0
0
votes
1
reply
774
views
Create Annotation for Long Read Nanopore Rna-Seq Data
Nanopore Annotation Rna-Seq
updated 4.4 years ago by 154k • written 4.4 years ago by ▴ 40
0
votes
0
replies
1.1k
views
Minor Allele Frequency error when running imputation using Beagle 5.2
Beagle
4.4 years ago by nad7wf • 0
0
votes
2
replies
1.0k
views
How to convert vcf file of GA100K data into bfile ie. .bed, .bim, .fam?
VCF
4.4 years ago by Rudra • 0
1
vote
5
replies
1.4k
views
How to calculate SNP frequency for each population in bfile using plink?
Frequency
updated 4.4 years ago by 45k • written 4.4 years ago by • 0
2
votes
1
reply
920
views
Study variation of some genes by VCF file
VCF mutation
updated 4.4 years ago by 45k • written 4.4 years ago by ▴ 110
0
votes
0
replies
900
views
News: Online Training - RADseq data analysis course
RADseq
4.4 years ago by Physalia-courses ★ 2.6k
0
votes
0
replies
999
views
freebayes produces gvcfs with shifted CHROM entries
gvcf SNP-call freebayes
4.4 years ago by johanna.pieplow • 0
1
vote
4
replies
2.6k
views
How to generate single sequence from assembled contigs?
assembly contigs genomics
updated 4.4 years ago by ★ 2.9k • written 4.4 years ago by ▴ 80
1
vote
2
replies
1.2k
views
Any pipeline/tool to predict fungal virulence factors ?
gene genome sequence
updated 2.3 years ago by 45k • written 4.4 years ago by ▴ 120
6
votes
3
replies
1.4k
views
Forum: Asking for content suggestions for updated bioinformatics book
python
updated 4.4 years ago by 89k • written 4.4 years ago by ▴ 690
121,983 results • Page 642 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
Answer: Nextflow MultiQC runs multiple times due to FASTQC zip name collisions
Comment: When to merge RNA-seq files with multiple sequencing lanes
Answer: When to merge RNA-seq files with multiple sequencing lanes
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Answer: Best set of tools / workflows for predicting the biosynthesis pathways of comple by ehaag ▴ 100
I tried [searching for tools in the NIAID Data Ecosystem][1] and found something that may be relevant. [PathPred][2] is an enzyme catalyzed…
Answer: Tools to simulate Illumina short read sequences and ONT long reads with a refere by ehaag ▴ 100
I did a quick [search for tools in the NIAID Data Ecosystem][1] and found a few that map Illumina short reads onto a reference genome, incl…
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…
Comment: convert genome file to transcriptome file by Ales ▴ 50
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…
Answer: GUI commercial software for 10x single cell gene expression analysis by Nicole • 0
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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