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121,999 results • Page 267 of 2440
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1
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5
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1.7k
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Any tutorial how to "link" SNPs with genes?
SNP
updated 2.5 years ago by ★ 3.1k • written 2.5 years ago by ▴ 20
1
vote
1
reply
884
views
Can I add labels to (some) cells in a plotColData from scater?
single-cell-experiment plotColData scater
2.5 years ago by Assa Yeroslaviz ★ 1.9k
0
votes
0
replies
617
views
how to set cutoff for the gage enrichment results value of stat.mean
enrichment gage cutoff stat.mean
2.5 years ago by alwayshope ▴ 40
0
votes
0
replies
705
views
Too many differential peaks derived from FindMarkers() [Signac]
Signac ATAC scATAC-seq
2.5 years ago by bioinformatics.girl ▴ 30
0
votes
0
replies
940
views
RMA Normalization & Units
Normalization Lines Cell RMA Microarray
2.5 years ago by James ▴ 30
2
votes
1
reply
3.0k
views
How to install VEP plugins in conda environment
conda VEP plugin
updated 2.5 years ago by 13k • written 2.5 years ago by • 0
4
votes
6
replies
2.3k
views
Should you specify "-p" for paired end reads using featureCounts?
fastq rnaseq genomics
2.5 years ago by O.rka ▴ 750
1
vote
2
replies
1.0k
views
How to retain proteins with both start and stop codons, and remove those with internal stop codons from FASTA file ?
gene annotation
2.5 years ago by BioinfoBee • 0
0
votes
2
replies
1.6k
views
Help with my fasta filter python scrips
FASTA python chi2
2.5 years ago by Luis Carlos • 0
9
votes
5
replies
1.7k
views
Tool for detecting valleys in Chip-seq like data?
NGS Chip-seq
updated 2.3 years ago by 45k • written 2.5 years ago by ▴ 20
1
vote
8
replies
2.5k
views
Same correlation values obtained at different soft threshold powers in WGCNA signed network analysis
sft wgcna langfelder
2.5 years ago by Aditi • 0
0
votes
0
replies
514
views
Is there available REGA or COMET versions for downloading & using on a local machine?
python subtyping recombination hiv
2.5 years ago by Mordovian Guy • 0
0
votes
2
replies
1.2k
views
Fastq deduplication levels
Sequence levels deduplication
updated 2.5 years ago by 154k • written 2.5 years ago by ▴ 120
2
votes
2
replies
1.4k
views
How to bin bed files (non-standard) into 10000bp window size?
bedtools makewindows
updated 2.3 years ago by 45k • written 2.5 years ago by ▴ 90
0
votes
1
reply
636
views
JGI bacterial image gallery
DOE gallery JGI images
updated 2.5 years ago by ★ 30k • written 2.5 years ago by ▴ 40
0
votes
5
replies
1.4k
views
Missing columns in meta table from SRA Selector
SRA esearch efetch
updated 2.5 years ago by 103k • written 2.5 years ago by • 0
0
votes
2
replies
866
views
Questions about DESeq and GOenrichment analysis for tomato
GOenrichment DESeq tomato
updated 2.4 years ago by 45k • written 2.5 years ago by • 0
3
votes
4
replies
3.2k
views
annotation_names_side does not work in complexheatmap package
complexheatmap
2.5 years ago by Aki ▴ 20
1
vote
3
replies
2.5k
views
How to demultiplex data with totalseq B antibodies using hashsolo?
cellranger. seq hashsolo rna
2.5 years ago by bioinfo ▴ 160
0
votes
0
replies
505
views
What is the limit of partition incompleteness?
beast mcmc phylogenetics bayesian
2.5 years ago by Mordovian Guy • 0
0
votes
2
replies
1.1k
views
How combine geom-point with geom-line?
R ggplot2
updated 2.2 years ago by 45k • written 2.5 years ago by ▴ 350
2
votes
3
replies
1.2k
views
Spatial transcriptiome analysis
Spatial Transcriptome Genome Cell Single
2.5 years ago by siu ▴ 160
1
vote
2
replies
1.1k
views
Extract CDS reads from a BAM file
samtools BAM BED
updated 2.3 years ago by 45k • written 2.5 years ago by • 0
5
votes
2
replies
2.8k
views
LIMMA: where to find the ANOVA?
bioconductor LIMMA R
2.5 years ago by Sebastian Hesse ▴ 350
1
vote
1
reply
1.6k
views
Right assay and slot for the extraction of normalized data after "sct normalization" and "anchor based integration"
single normalization integration cell sct anchor seurat based
updated 2.5 years ago by ★ 1.9k • written 2.5 years ago by ▴ 260
2
votes
0
replies
1.2k
views
Herald: The Biostar Herald for Monday, April 24, 2023
herald
2.5 years ago by Biostar 3.6k
0
votes
1
reply
1.5k
views
Why does Guppy output different sequence data (same model)?
guppy Nanopore
updated 2.5 years ago by 154k • written 2.5 years ago by • 0
2
votes
2
replies
1.2k
views
Error in measuring percentage of mit.genes
scRNA-seq bug seurat
updated 2.5 years ago by 154k • written 2.6 years ago by • 0
8
votes
10
replies
10k
views
ANI calculation: alternatives to Jspecies
ani jspecies
updated 2.5 years ago by 8.0k • written 10.4 years ago by ▴ 620
0
votes
3
replies
1.1k
views
How do i figure out whether a recognition site is conserved or not?
Emboss Restriction-Electrophoresis Restrict pcr-rflp 16s-rRNA
2.5 years ago by Mahmoud Reda ▴ 10
0
votes
2
replies
989
views
My nexus file can be displayed in R, but can not in Figtree
beast figtree
2.5 years ago by wukunouc • 0
0
votes
0
replies
465
views
plotProfile weird methylation fraction
methylation plotprofile Methyldackel extractor
2.5 years ago by Mario • 0
0
votes
0
replies
454
views
Multi-mapping read adjacency in alignment tool outputs
aligners multi-mapping alignments
2.5 years ago by Alex • 0
1
vote
7
replies
3.8k
views
A large portion of gene ID cannot be mapped when running the "bitr" command of the "clusterProfiler" package
scRNA-seq Seurat GSEA
updated 2.5 years ago by 13k • written 2.5 years ago by ▴ 110
3
votes
3
replies
1.3k
views
GATK error on HPC clusters
variant-calling SNP
updated 18 months ago by 45k • written 2.5 years ago by • 0
1
vote
0
replies
659
views
News: Course - Statistics for biologists with R
Statistics R
2.5 years ago by Physalia-courses ★ 2.6k
1
vote
2
replies
1.0k
views
What is the standard of validating differentially expressed genes experimentally from scRNA seq analyses?
scRNA single-cell
updated 22 months ago by 45k • written 2.5 years ago by • 0
2
votes
2
replies
997
views
Drosophila, dbSNP, GATK
SNP GATK Drosophila
2.4 years ago by Kirill • 0
1
vote
3
replies
2.2k
views
How do I project known tSNE coordinates onto SeuratObject
scRNAseq project single-cell-RNA-seq seurat embeddings
updated 2.5 years ago by 4.2k • written 2.5 years ago by ▴ 10
0
votes
0
replies
474
views
Double coverage peak for targeted sequencing
targeted sequencing Illumina NGS
2.5 years ago by tramelliwe • 0
0
votes
3
replies
1.5k
views
How to make barplots for multi sample gene ontology analysis
enrichment-analysis GO
updated 2.5 years ago by ▴ 10 • written 2.5 years ago by ▴ 20
0
votes
1
reply
1.5k
views
Normalization of ChIP-seq results with deepTools
ChIP-seq deepTools normalization
updated 2.5 years ago by 89k • written 2.5 years ago by • 0
0
votes
3
replies
1.4k
views
Chance that DNA with 3N nucleotide encodes 2 protein with size of N amino-acids in different frames?
probability DNA estimation statistics proteins
updated 2.5 years ago by 4.2k • written 2.5 years ago by ▴ 10
1
vote
1
reply
790
views
Featurecounts countmatrix creation
featurecounts DEA bamfile
updated 2.5 years ago by 13k • written 2.5 years ago by • 0
2
votes
1
reply
961
views
Randomly reduce size of reads but preserving the distribution
sequencing biostatistics
updated 2.5 years ago by 8.7k • written 2.5 years ago by ▴ 70
3
votes
7
replies
4.7k
views
HISAT2 relaxing parameters?
RNA-Seq HISAT2 alignment mapping mismatches
updated 2.5 years ago by ★ 2.1k • written 7.3 years ago by ▴ 10
1
vote
2
replies
892
views
color key heatmap
heatmap
2.5 years ago by kalyani ▴ 10
6
votes
2
replies
2.7k
views
R and R studio for Macbook
studio R
updated 2.5 years ago by ▴ 30 • written 2.5 years ago by • 0
0
votes
0
replies
657
views
Gene Expression Database for Mental Disorders
gene_expression_db
2.5 years ago by leenkhoury282 • 0
0
votes
0
replies
996
views
illuminaHumanv2.db returning NA for all Illumina probe ID to gene symbol conversion
microarray illumina R probe-annotation
2.5 years ago by accibio ▴ 20
121,999 results • Page 267 of 2440
Recent Votes
Difficulty running FoldX in linux
Answer: Difficulty running FoldX in linux
Answer: Differences between published differential gene expression results and own analy
Answer: Differences between published differential gene expression results and own analy
Comment: Problems with PacBio's Improved Phased Assembler (IPA)
Comment: Differences between published differential gene expression results and own analy
A: Fold change - a final explanation
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Recent Replies
Comment: headers missing in efetch results for SRA database by Leela • 0
Please note that this is still a problem in the recent version in `conda` (v24.0)
Comment: Difficulty running FoldX in linux by strayeroliver • 0
Thank you very much for your help.
Comment: Problems with PacBio's Improved Phased Assembler (IPA) by Billy Rowell ▴ 520
Completely understand. I hope this helps then!
Comment: Checkm results differ from database info by Mensur Dlakic ★ 30k
Impossible to answer with the little information you provided. It's like saying that your soufflé didn't rise, and we are supposed to guess…
Comment: Active site using castpfold by Mensur Dlakic ★ 30k
Please don't take my comment the wrong way. Docking ligands is a serious endeavor that includes many preparatory steps, a use of highly so…
Comment: Problems with PacBio's Improved Phased Assembler (IPA) by Panos ★ 1.8k
Thanks! I will try further downgrading snakemake (and python).. Actually, I have already tried `hifiasm` which worked perfectly (as always…
Comment: downloading raw bam files from pacbio sequencer by GenoMax 154k
https://www.biostars.org/u/151541/ look through some of the top entries from this search for subread BAM's. Here is one example: https://do…
Comment: Difficulty running FoldX in linux by Mensur Dlakic ★ 30k
I think `1ubq_Repair_1.pdb` is an intermediate file, and the other 3 files matter. But I use FoldX rarely, so you will have to verify this …
Comment: Difficulty running FoldX in linux by strayeroliver • 0
That's great, @mensur. Thank you. I have a run that operates on 1ubq_Repair.pdb and produces a 'Dif_1ubq_Repair.fxout' now, even with numbe…
Comment: Problems with PacBio's Improved Phased Assembler (IPA) by Billy Rowell ▴ 520
Is there a reason you'd like to use IPA over, for instance, hifiasm? I'd recommend starting with hifiasm. For pbipa, try downgrading to s…
Answer: Active site using castpfold by dthorbur ★ 3.1k
This is very similar to your recent [post](https://www.biostars.org/p/9615406/) - if you aren't going to provide the protein example for a …
Answer: Differences between published differential gene expression results and own analy by Zhenyu Zhang ★ 1.3k
1. When you said "the same dataset", are you sure about the files are the same, or you just mean the same list of patients? There are many …
Answer: downloading raw bam files from pacbio sequencer by Arup Ghosh 3.4k
Try: https://www.google.com/search?q=site:https://downloads.pacbcloud.com/public/dataset/+%22subreads%22
Comment: downloading raw bam files from pacbio sequencer by GenoMax 154k
If they are not available at PacBio site then your chances of getting them are going to be significantly reduced. Only other source may be …
Comment: downloading raw bam files from pacbio sequencer by pranavdatar01 • 0
Yes, I did check. They don't have any.
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