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122,199 results • Page 647 of 2444
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10
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11
replies
6.2k
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Help with rownames in DESeq2
DESeq2 DEG Rstudio R
updated 4.5 years ago by • 0 • written 4.5 years ago by ▴ 10
0
votes
0
replies
827
views
News: Event: Women in data science and bioinformatics - perspectives from industry and academia
gender women equality event data-science
updated 4.4 years ago by 45k • written 4.5 years ago by ▴ 470
4
votes
2
replies
1.6k
views
Use TPM to compare between the samples
TPM Analysis RNA-seq DE
4.5 years ago by Kunal • 0
1
vote
5
replies
4.1k
views
SNPs file for reference genome (Mouse - GRCm39)
Mouse SNPs Rna-seq Genome GRCm39
4.5 years ago by David Martínez ▴ 10
1
vote
10
replies
3.3k
views
Help with mitochondrial sequences from GenBank!!!
ftp genbank mitochondrial
4.5 years ago by Matteo Ungaro ▴ 130
0
votes
0
replies
960
views
Job: ELIXIR/EMBL-EBI: Front-end or full-stack web developer
front-end web-developer data FAIR
updated 4.4 years ago by 45k • written 4.5 years ago by ▴ 470
0
votes
0
replies
1.1k
views
Job: ELIXIR/EMBL-EBI: Project Manager/Senior Project Coordinator - COVID-19
EMBL-EBI project data COVID-19 COVID management
4.5 years ago by Erin Haskell ▴ 470
0
votes
4
replies
1.3k
views
Mutation Software
Mutation
updated 4.4 years ago by ★ 90k • written 4.5 years ago by • 0
0
votes
1
reply
872
views
RNA-seq: extraction and annotation of differentially expressed genes
RNAseq Galaxy DEG analysis
updated 4.5 years ago by 9.0k • written 4.5 years ago by ▴ 10
8
votes
8
replies
3.4k
views
Do I need Illumina Demultiplexing for RNASeq?
Demultiplexing Galaxy RNASeq
updated 4.5 years ago by 154k • written 4.5 years ago by ▴ 20
2
votes
1
reply
2.6k
views
Creating a haplotype map now that the HapMap site has been taken down
HapMap
updated 4.5 years ago by • 0 • written 9.3 years ago by ▴ 10
5
votes
10
replies
6.5k
views
9 follow
Error ecountered while running conifer with demo data set
conifer python numpy cnv
updated 4.5 years ago by ▴ 20 • written 8.4 years ago by ▴ 10
2
votes
1
reply
961
views
STRINGdb "Expected Interactions"?
STRINGdb
updated 4.5 years ago by ★ 30k • written 4.5 years ago by ▴ 30
4
votes
4
replies
2.7k
views
How much weights a million reads
sequencing
4.5 years ago by gubrins ▴ 350
0
votes
4
replies
1.2k
views
Gene-filterin In R
R
4.5 years ago by soniabedi.07 ▴ 30
4
votes
3
replies
3.3k
views
STAR Aligner --quantMode GeneCounts
RNA-Seq STAR
updated 4.5 years ago by 15k • written 4.5 years ago by ▴ 80
2
votes
2
replies
4.1k
views
Extract chromosome 1 - 22 ,X and Y from BAM file
NGS
updated 4.5 years ago by 14k • written 4.5 years ago by ▴ 40
0
votes
0
replies
687
views
Haplotype inference algorithms in Pedigrees
algorithms pedigree inference snps haplotype
4.5 years ago by S. Roa ▴ 10
2
votes
1
reply
1.6k
views
What does “non-log-linear space” mean for genomic data?
Data
updated 4.5 years ago by 11k • written 4.5 years ago by ▴ 10
0
votes
4
replies
2.1k
views
ComplexHeatmap Package takes forever to plot
ComplexHeatmap heatmap
updated 4.5 years ago by 21k • written 4.5 years ago by • 0
0
votes
0
replies
660
views
Differentiating alleles from paralogs in comparison of transcriptomes within species
clustering transcriptome paralog trinity assembly
4.5 years ago by jfaberha ▴ 50
2
votes
2
replies
1.0k
views
Concatenate multifastas
join fasta concatenate multifasta
4.5 years ago by Colaptes ▴ 120
0
votes
2
replies
2.9k
views
TCGA-BRCA downloading issue by GDCquery
TCGABiolinks TCGA-BRCA
updated 2.7 years ago by 45k • written 4.5 years ago by • 0
2
votes
3
replies
2.9k
views
merging two VCF files
gatk dictionary vcf
updated 4.5 years ago by ▴ 480 • written 4.5 years ago by ▴ 110
0
votes
0
replies
553
views
Tools to view pacbio assembly
genome
4.5 years ago by K ▴ 10
1
vote
4
replies
5.5k
views
Reasons For Low Ts/Tv Ratio
exome snp
written 14.2 years ago by ▴ 110
2
votes
1
reply
2.0k
views
gffcompare class_code "u"
gffcompare
updated 4.5 years ago by ▴ 290 • written 4.5 years ago by • 0
0
votes
4
replies
3.3k
views
Low Counts with featureCounts
RNA-Seq featureCounts
updated 4.5 years ago by ▴ 290 • written 5.3 years ago by • 0
2
votes
3
replies
2.2k
views
How we can use DEG data for GSEA analysis
GSEA
4.5 years ago by yeshiwork2000 • 0
0
votes
1
reply
836
views
Create Annotation for Long Read Nanopore Rna-Seq Data
Nanopore Annotation Rna-Seq
updated 4.5 years ago by 154k • written 4.5 years ago by ▴ 40
0
votes
0
replies
1.1k
views
Minor Allele Frequency error when running imputation using Beagle 5.2
Beagle
4.5 years ago by nad7wf • 0
0
votes
2
replies
1.1k
views
How to convert vcf file of GA100K data into bfile ie. .bed, .bim, .fam?
VCF
4.5 years ago by Rudra • 0
1
vote
5
replies
1.5k
views
How to calculate SNP frequency for each population in bfile using plink?
Frequency
updated 4.5 years ago by 45k • written 4.5 years ago by • 0
2
votes
1
reply
991
views
Study variation of some genes by VCF file
VCF mutation
updated 4.5 years ago by 45k • written 4.5 years ago by ▴ 110
0
votes
0
replies
938
views
News: Online Training - RADseq data analysis course
RADseq
4.5 years ago by Physalia-courses ★ 2.7k
0
votes
0
replies
1.1k
views
freebayes produces gvcfs with shifted CHROM entries
gvcf SNP-call freebayes
4.5 years ago by johanna.pieplow • 0
1
vote
4
replies
2.7k
views
How to generate single sequence from assembled contigs?
assembly contigs genomics
updated 4.5 years ago by ★ 2.9k • written 4.5 years ago by ▴ 80
1
vote
2
replies
1.2k
views
Any pipeline/tool to predict fungal virulence factors ?
gene genome sequence
updated 2.4 years ago by 45k • written 4.5 years ago by ▴ 120
6
votes
3
replies
1.5k
views
Forum: Asking for content suggestions for updated bioinformatics book
python
updated 4.5 years ago by 90k • written 4.5 years ago by ▴ 690
1
vote
4
replies
1.6k
views
gene expression for a specific gene across for multiple cancer types in TCGA datasets
gene_expression TCGA RTCAG
4.5 years ago by pt.taklifi ▴ 70
0
votes
4
replies
4.2k
views
Flye assembly of a bacterial genome stuck
assembly Flye
updated 4.5 years ago by 3.9k • written 4.5 years ago by ▴ 180
2
votes
4
replies
7.4k
views
Difficulty filtering VCF file with vcftools
SNP
updated 4.5 years ago by ▴ 480 • written 9.1 years ago by ▴ 110
1
vote
2
replies
2.1k
views
KING relatedness inference working way too long...
large-cohort
4.5 years ago by German.M.Demidov ★ 3.0k
0
votes
4
replies
1.9k
views
Issue with memory and the gcsa index in toil-vg
toil-vg vg vgteam
4.5 years ago by jcmouren • 0
0
votes
2
replies
1.1k
views
RNA-seq different reads numbers of two samples is trouble?
RNA-Seq R seq python linux
updated 4.5 years ago by ★ 1.4k • written 4.5 years ago by ▴ 10
0
votes
0
replies
838
views
How to merge the mutations from multiple samples of one patient
MutSig2CV_NC MutSig2CV cancer mutation merge
4.5 years ago by Rongxin ▴ 40
0
votes
9
replies
4.1k
views
Using wildcards in function in rules
snakemake rules wildcards
updated 4.5 years ago by ▴ 160 • written 4.5 years ago by ▴ 10
4
votes
7
replies
5.9k
views
6 follow
Tool: MAGERI: a software tool for calling rare variants and detecting circulating tumor DNA from UMI-tagged high-throughput sequencing data
rare-variant resequencing umi ctDNA
updated 21 months ago by • 0 • written 8.6 years ago by 3.5k
0
votes
0
replies
950
views
Avoid genome circularization with Canu assembler
circularization ONT Canu repetitive-regions assembler
updated 19 months ago by 45k • written 4.5 years ago by • 0
0
votes
1
reply
1.1k
views
read ids along with transcript ids
stringtie flair read correction nanopore
updated 4.5 years ago by 103k • written 4.5 years ago by • 0
122,199 results • Page 647 of 2444
Recent Votes
Comment: Can i use orthofinder for small protein datasets and not full proteome?
Answer: Can i use orthofinder for small protein datasets and not full proteome?
Answer: Can i use orthofinder for small protein datasets and not full proteome?
Answer: Midpoint rooting IQTREE newick file moves node support around
Answer: Subsetting before QC in Spatial Transcriptomics
Answer: Feature Counts vs Salmon quantification
Comment: Feature Counts vs Salmon quantification
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Popular Question to colindaven 8.1k
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Recent Replies
Comment: Can i use orthofinder for small protein datasets and not full proteome? by alexandrakortsi • 0
By sequence. Thank you for your response!
Comment: Why did the QV value decrease significantly after using YAHS for HiC scaffolding by xinguok794 ▴ 10
Thank you for your reply! Unfortunately, despite running YAHS with `--no-contig-ec`, the QV value of the resulting FASTA file did not impro…
Comment: Subsetting before QC in Spatial Transcriptomics by Kent ▴ 30
Hi Kevin, Thanks for the detailed explanation. Due to the characteristics of the datasets, we initially used very lenient quality control…
Comment: Midpoint rooting IQTREE newick file moves node support around by Luca Arbore ▴ 10
Thank you very much Kevin, it worked!
Comment: ID unifiying across different datasets by GenoMax 154k
In this case the entry notes that this is likely the product of a pseudogene: https://www.uniprot.org/uniprotkb/Q5VTE0/entry and existence …
Comment: Comparison of different RNAseq data sets by DrSmad ▴ 10
Each lab contributes both control and LPS. Example, for cell line A_lab1 did and analysis on control and LPS-6h. Cell line B_lab2 did contr…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
sorry, why some gene names are often lacking though the Uniprot ID is still valid (using biomart)?
Comment: snpEff: Unsupported structural variant types by shpak.max ▴ 70
Unfortunately, while it ran without a problem initially, when I checked the run screen today, I saw the following error message (and unlike…
Comment: ID unifiying across different datasets by GenoMax 154k
You can use the [**ID mapping tool**][1] from UniProt site (third ID did not map from the list above): From To P68104 ENSG0000015…
Answer: The geo samples is not having sentrix id and sentrix position. But this informat by yura.grabovska ▴ 890
Crosspost from related question: https://www.biostars.org/p/9616466/#9616534 ``` ##Using R, illuminaio from Bioconductor library(…
Answer: Finding Sentrix ID in HM450K arrays by yura.grabovska ▴ 890
``` ##Using R, illuminaio from Bioconductor library(illuminaio) temp.idat <- readIDAT(file = "200379120087_R02C02_Grn.idat") tem…
Comment: Can i use orthofinder for small protein datasets and not full proteome? by michael.ante ★ 4.0k
Do you want to compare them by sequence or by function? For the later, you can use e.g. InterProScan, KoFamScan.
Answer: Can i use orthofinder for small protein datasets and not full proteome? by dthorbur ★ 3.2k
If you're just using the tool for clustering purposes, I think OrthoFinder might be a little clunky and would recommend using something lik…
Comment: ID unifiying across different datasets by zizigolu ★ 4.4k
Thank you; The problem is let's say in the protein ID column I see `Q5VTE0;P68104;Q05639` here I am sure I should get which `ENSG` for eac…
Comment: How to improving 2-Nucleotide RNA-seq Mapping Accuracy by 2411110159 • 0
Since we do not have real data yet, I tried to simulate this using strand-specific RNA bisulfite-seq reads (C to T). Read1 corresponds to t…
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