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121,904 results • Page 31 of 2439
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468
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cytAssist manual alignment failing for visium HD and spaceranger count
spatial-transcriptomics visiumhd space-ranger
updated 6 months ago by 153k • written 6 months ago by ▴ 20
2
votes
5
replies
890
views
Nanopore specific assembly tool of Mitochondria
Assembly Nanopore Mitochondria
updated 6 months ago by 7.9k • written 6 months ago by ▴ 60
7
votes
21
replies
9.8k
views
6 follow
install Bioconductor package and its dependencies
Bioconductor R
updated 6 months ago by • 0 • written 7.4 years ago by ▴ 420
0
votes
1
reply
479
views
Biostars API Issues
visualization web-scraping api
updated 6 months ago by 45k • written 6 months ago by • 0
0
votes
0
replies
274
views
interpret ligand_receptor pairs
pairs Ligand multinichenetr receptor
6 months ago by mayahammoud161 • 0
5
votes
7
replies
2.0k
views
DESeq2: error in checkFullRank(modelMatrix)
DESeqDataSet design DESeq2 RNA-Seq
updated 6 months ago by • 0 • written 10 months ago by • 0
1
vote
6
replies
732
views
Comparability between normalized Counts / TPMs and log2FoldChange
FoldChange TPMs DESeq2 normalized RNAseq counts
6 months ago by NorbertK ▴ 10
0
votes
1
reply
500
views
Assistance Required: Error with MuSiC2 Package - "pVar" Function Not Found
MuSiC2
updated 6 months ago by 6.5k • written 6 months ago by • 0
5
votes
2
replies
1.1k
views
Forum: Do you agree with the practice of combing TCGA with GTEx?
GTEx TCGA
updated 6 months ago by 22k • written 6 months ago by ▴ 40
1
vote
7
replies
1.6k
views
Help with Funannotate
genomes funannotate fungus annotation
updated 6 months ago by 15k • written 6 months ago by ▴ 240
1
vote
2
replies
550
views
Annotations Tools
annotations for Tools
6 months ago by abebe1423 • 0
1
vote
3
replies
717
views
Alphafold in colab - homotrimer
Homotrimer
updated 6 months ago by ★ 3.1k • written 6 months ago by • 0
0
votes
0
replies
318
views
Different results with 'clara-parabricks fq2bam' and bowtie2
fq2bam clara-parabricks fastq bowtie2
6 months ago by Lars • 0
0
votes
0
replies
324
views
GWAS to gene function prediction
annotation vcf gwas prediction gene
6 months ago by alnus • 0
5
votes
2
replies
607
views
miRNAs - Adapters, adapters, adapters i´m so confused
miRNA-seq GEO Adpaters miRNAs
updated 6 months ago by 45k • written 6 months ago by ▴ 40
1
vote
2
replies
561
views
DEseq2: Advice for model (double interaction ?)
deseq2 matrix dge
6 months ago by Picasa ▴ 690
0
votes
1
reply
469
views
Kallisto alignment with HPC (SLURM)
slurm hpc kallisto alignment
updated 6 months ago by ★ 7.7k • written 6 months ago by • 0
0
votes
0
replies
247
views
KEGG pathways
KEGG Pathways
6 months ago by Blue • 0
2
votes
4
replies
932
views
Protein-Protein Network
Cytoscape Genes Breast-Cancer Network
updated 6 months ago by 45k • written 6 months ago by • 0
0
votes
5
replies
1.4k
views
Correct format for Hi-C matrix before converting to BEDPE
juicer matrix bedpe HI-C
updated 6 months ago by ▴ 380 • written 6 months ago by • 0
0
votes
0
replies
366
views
News: Mass Spectrometry and Proteomics using R and Bioconductor course
R Bioconductor Mass-Spectrometry Proteomics
updated 6 months ago by 45k • written 6 months ago by ★ 2.6k
0
votes
0
replies
311
views
How to download data from MGRAST
MGRAST microbiome metagenome
6 months ago by Maxwell ▴ 70
0
votes
2
replies
613
views
Gene level expression versus variant-level expression
variant RNASeq
6 months ago by ramiro.barrantes ▴ 60
1
vote
1
reply
505
views
Java error in BEAST2
BEAST2 java
updated 6 months ago by 166k • written 6 months ago by • 0
1
vote
10
replies
4.2k
views
Bedmethyl file format
bedmethyl methylation
updated 6 months ago by • 0 • written 17 months ago by ▴ 20
0
votes
4
replies
937
views
Tool: PIASO, a python toolkit for single-cell data analysis
data-integration scRNA-seq normalization scATAC-seq spatial-transcriptomics
6 months ago by Min • 0
12
votes
6
replies
2.4k
views
Forum: What is the current state of the beef against UMAP/tSNE in the context of sc trajectory analysis/monocle3?
monocle3 umap single-cell tSNE trajectory
6 months ago by txema.heredia ▴ 250
1
vote
1
reply
645
views
Type of Pangenome Type/program to use for fungal isolates of the same species, but have major translocations
visualization pangenome genome alignment
updated 6 months ago by ▴ 600 • written 6 months ago by ▴ 10
0
votes
0
replies
295
views
Finding Indel Mutant structures
indel
6 months ago by Logan • 0
0
votes
0
replies
367
views
Doublet Detection for Intestinal Immune Cells in scRNA-seq
scDblFinder Seurat scRNA-seq Doublets Immune
6 months ago by s • 0
4
votes
7
replies
3.3k
views
Compare genomes of different species and published studies (different years, sequencing technologies...) is correct?
comparative-genomics
updated 6 months ago by ▴ 70 • written 7 months ago by • 0
1
vote
1
reply
631
views
no "-" strand in transcriptome alignment
DRS transcriptome alignment
updated 6 months ago by 153k • written 6 months ago by ▴ 60
0
votes
3
replies
1.0k
views
What is best way to do CNV Analysis on Xenium data (Spatial transcriptomics)?
seurat xenium spatialtranscriptomics singlecell
updated 6 months ago by ▴ 820 • written 6 months ago by ▴ 20
2
votes
3
replies
807
views
Finding a gene in human
variant gene
updated 6 months ago by 45k • written 6 months ago by ★ 4.4k
4
votes
4
replies
1.1k
views
Assigning cell annotation based on calculated scores.
Clustering Seurat UCell cell-annotations Score
updated 6 months ago by 89k • written 6 months ago by ★ 1.9k
0
votes
0
replies
326
views
single cell rna seq NMF Error in which.min(sapply(res.runs, "[[", "residuals"))
error sc-rna-seq Seurat NMF
updated 6 months ago by 6.5k • written 6 months ago by • 0
1
vote
1
reply
551
views
Low quality of NGS SNP analysis panel
fastqc iontorrent ngs
updated 6 months ago by ▴ 290 • written 6 months ago by • 0
2
votes
4
replies
975
views
Multiple fail points in fastqc file
fastqc report
6 months ago by dr.deepakkukkar • 0
2
votes
1
reply
577
views
mapping to transcriptome.fasta vs genome.fasta
mapping gtf transcriptome genome
updated 6 months ago by ★ 30k • written 6 months ago by ▴ 60
0
votes
2
replies
524
views
Where to find WGS, metagenome data for obesity group?
HMP microbiome data NCBI metagenomics
updated 4 months ago by ▴ 100 • written 6 months ago by ▴ 70
1
vote
2
replies
639
views
WDL 1.0 - Directory Type
directory input wdl
6 months ago by davidmaimoun ▴ 50
0
votes
1
reply
547
views
How to input INDELs in ped files
SNP R haplostats Haploview INDEL
updated 3 months ago by • 0 • written 6 months ago by ▴ 40
1
vote
0
replies
357
views
Tool: HGVSV: A tool to parse and generate HGVS names with Structural Variant support
Variants HGVSV Variant HGVS Structural
6 months ago by parker.payne ▴ 10
0
votes
3
replies
898
views
P-value calculation between groups in split violin plot
violinplot ggplot singlecellRnaseq
updated 6 months ago by 5.1k • written 6 months ago by ▴ 390
0
votes
2
replies
935
views
After doublet detection in 10x scRNA-Seq data, there is still evidence of doublets
R DoubletFinder Seurat scRNA
updated 6 months ago by ★ 1.7k • written 6 months ago by ▴ 820
0
votes
0
replies
366
views
Hash-Based Allele Calling
calling hash allele
6 months ago by davidmaimoun ▴ 50
0
votes
0
replies
301
views
Issues with FPKM Calculation in RNA-seq Analysis (Apodemus agrarius)
FPKM. Cufflinks
updated 6 months ago by 15k • written 6 months ago by ▴ 40
2
votes
5
replies
970
views
Metagenomics/amplicon sequencing: Most publicly available data already host removed sequences or no?
amplicon decontamination QC Microbiome metagenomics
6 months ago by Maxwell ▴ 70
0
votes
1
reply
501
views
plot PLINK2.0 output with ggtree
ibs matrix plink ggtree
6 months ago by Matteo Ungaro ▴ 130
4
votes
3
replies
2.1k
views
Boltz1 structure prediction software installation
boltz1
updated 6 months ago by ▴ 40 • written 7 months ago by ▴ 10
121,904 results • Page 31 of 2439
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Answer: Tried building a compact sequence format with 4-bit storage
Tried building a compact sequence format with 4-bit storage
Shift in RNA 3' position, Term-Seq vs RNASeq
Comment: STARlong for pacbio Isoseq reads
Comment: Automatically annotating a feature using a genbank file
Answer: Is this PCA plot correct??
Answer: Is this PCA plot correct??
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Comment: Is total miRNA in EV constant? Implications for library size normalization. by Gordon Smyth ★ 8.3k
RNA-seq is very good at relative analyes. It would be straightforward to determine which miRNAs are relatively more abundant, compared to o…
Comment: Tried building a compact sequence format with 4-bit storage by Pranava ▴ 10
Woah!!! Thank you very much, Matthias. I honestly didn't even know some of those existed and I will definitely go through them and try to u…
Answer: Tried building a compact sequence format with 4-bit storage by Matthias Zepper 5.1k
Hello Pranava, Thanks for sharing your repository. Devising a new file format is an interesting undertaking and certainly a task with many…
Answer: Gene Ontology Enrichment with LOC gene IDs in Common Carp (Cyprinus carpio) by GenoMax 153k
`LOC` gene ID's are often assigned to uncharacterized genes and you may not get useful information from databases for them, thus they will …
Comment: Whole Genome Sequencing IG regions by GenoMax 153k
> are the calls I am seeing reliable or should I take them with something of a pinch of salt? Not sure what calls you are referring to but…
Comment: RNA-SEQ where only a subset of genes is of interest by piffelpaff • 0
Sorry to revive this ancient thread but I'm currently discussing the same question with some people in my lab and would love to somebody po…
Answer: STARlong for pacbio Isoseq reads by YuZJ • 0
Hello, you may try deSALT (DOI: 10.1186/s13059-019-1895-9, GitHub: ydLiu-HIT/deSALT) or uLTRA (DOI: 10.1093/bioinformatics/btab540, GitHub:…
Comment: Shift in RNA 3' position, Term-Seq vs RNASeq by acvill ▴ 350
Without knowing the details of the Term-seq method, could the 38 nt shift be accounted for by the difference in the position of the ribosom…
Comment: STARlong for pacbio Isoseq reads by Buffo ★ 2.4k
Thanks, I'll give it a try.
Comment: STARlong for pacbio Isoseq reads by GenoMax 153k
You could give `mapPacBio.sh` from BBMap suite a try while you wait for other answers. That works for reads up to 6 kb. BBMap has a new hom…
Comment: STARlong for pacbio Isoseq reads by Buffo ★ 2.4k
The average is 1.8kb. I was planning to post it on GitHub, but it seems like the repository has been unattended for the last months, so I d…
Comment: Getting just fastqc.zip file? by GenoMax 153k
Yes, You can either use it on command line or use the graphical user interface.
Comment: STARlong for pacbio Isoseq reads by GenoMax 153k
What is the average length of your reads? That error sounds like a bug, so you may want to post that on `STAR` repo as an issue. I assume …
Comment: Getting just fastqc.zip file? by pourhangleila95 • 0
I want to perform fastQC on my data.Do you use fastQC software for doing it?
Comment: Whole Genome Sequencing IG regions by 719 • 0
Sorry for the poor wording of the original post, also should say I really appreciate people taking a moment to look at my post. My main con…
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