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270 results • Page 2 of 6
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1
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2.3k
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Shannon vs Simpson for TCR diversity estimation
TCR shannon simpson
updated 4 days ago by 81k • written 5.0 years ago by ▴ 750
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq bulk-RNASeq RNA-Seq single-cell
updated 5 days ago by • 0 • written 3.8 years ago by ★ 1.8k
4
votes
5
replies
1.9k
views
which package should be selected for differential gene expression analysis
Differential-gene-expression RNA-Seq
updated 6 days ago by 43k • written 5.5 years ago by ▴ 100
2
votes
5
replies
1.3k
views
Limma for paired and unpaired samples. Strange number of DEGs in unpaired samples
RNA-seq Limma Differential-gene-Expression R
updated 6 days ago by 43k • written 23 months ago by ▴ 70
5
votes
5
replies
829
views
Blacklist for bacterial genome [ChIPseq]?
ChIPseq Blacklist
updated 3 days ago by 43k • written 9 months ago by ▴ 30
8
votes
5
replies
1.2k
views
Classifying repeat features from Ensembl
ensembl repeat
updated 1 day ago by ▴ 190 • written 15 months ago by ★ 1.4k
9
votes
5
replies
2.2k
views
Millions of Reads Needed for Differential Gene Expression
differential-gene-expression RNA-Seq deseq2
updated 6 days ago by 43k • written 4.5 years ago by ▴ 20
3
votes
5
replies
412
views
Having trouble building VG in Ubuntu
vg
updated 2 days ago by 43k • written 5 days ago by • 0
37
votes
5
replies
13k
views
How do you generate TMM normalized counts using EdgeR?
R RNA-seq edgeR
updated 5 days ago by ▴ 60 • written 2.8 years ago by ★ 1.0k
1
vote
5
replies
316
views
samtools filtering
samtools
updated 5 days ago by ★ 1.2k • written 12 days ago by ▴ 70
1
vote
5
replies
243
views
Best way to deal with overlapping read names in merged BAM files
picard MarkDuplicates
17 hours ago by shpak.max ▴ 50
0
votes
5
replies
364
views
Used featureCounts to generate a count matrix for sc RNA-seq and it has all 0s.
scRNA-seq
updated 5 days ago by 141k • written 6 days ago by • 0
2
votes
5
replies
969
views
Ties in reranked list
fgsea GSEA
updated 2 days ago by • 0 • written 6 months ago by • 0
2
votes
5
replies
2.3k
views
DGE on transcriptomic data, focus on transcript sequences or in derivated ORFs?
differential-gene-expression RNA-Seq ORFs
updated 6 days ago by 43k • written 6.4 years ago by ▴ 90
0
votes
5
replies
1.2k
views
RNAseq differential gene expression analysis yield results which come from digestive content
differential-gene-expression RNA-Seq
updated 6 days ago by 43k • written 6.3 years ago by ▴ 90
1
vote
5
replies
2.8k
views
Batch effect identification using PCA
PCA qRT-PCR R targeted-assay Batch-Effect
updated 19 hours ago by 43k • written 3.8 years ago by ▴ 250
3
votes
5
replies
1.3k
views
How to identify antibiotic resistant genes in gene databases?
antibiotic Gene-Ontology GO
updated 4 days ago by 43k • written 2.0 years ago by • 0
5
votes
5
replies
486
views
NCBI MEGABLAST versus UCSC BLAT
blast blat alignment megablast
updated 6 days ago by ▴ 490 • written 7 days ago by ▴ 40
3
votes
4
replies
3.3k
views
Motif analysis of DMRs (Differentially Methylated Regions) by HOMER
next-gen
updated 4 days ago by 43k • written 6.7 years ago by ▴ 10
1
vote
4
replies
386
views
Database or Tool: Identifying Gene Regions (Exon/Intron/UTR) from Chromosome Position
gene-region biomart ucsc-browser intron exon
updated 6 days ago by 141k • written 6 days ago by • 0
0
votes
4
replies
298
views
Compute bootstrap values on consensus tree
phylogeny tree raxml
21 hours ago by pablo ▴ 300
3
votes
4
replies
266
views
BRAKER3 genome annotation
annotation BRAKER3 genome
updated 21 hours ago by ★ 2.4k • written 1 day ago by ▴ 20
4
votes
4
replies
333
views
Bowtie2 mapping is slow
metagenomics bowtie2 mapping read
updated 4 days ago by 6.3k • written 13 days ago by • 0
5
votes
4
replies
2.2k
views
How do we process Kallisto output (continuous real values) for DESEQ2 analysis (which strictly require discrete count values)?
read-counts DESEQ2 differential-gene-expression kallisto
updated 6 days ago by 43k • written 2.7 years ago by ▴ 170
2
votes
4
replies
281
views
Which command ro run MAKER pipeline for gene annotation ?
run. command to MAKERpipeline.
updated 1 day ago by 141k • written 1 day ago by ▴ 10
2
votes
4
replies
2.6k
views
DESeq2 inconsistent results
differential-gene-expression RNA-Seq DESeq2
updated 6 days ago by 43k • written 8.0 years ago by ▴ 80
4
votes
4
replies
431
views
Why number of interactions decreased in current string database for plasmodium
string interactions ppi
updated 4 days ago by ▴ 50 • written 4 days ago by ▴ 840
4
votes
4
replies
126
views
I'm new to cell ranger. Can single cells prepared with a protocol other than the 10x genomics protocol not be processed with cell ranger?
cellranger scRNA-seq 10x
3 hours ago by Spring • 0
0
votes
4
replies
328
views
How to use pre-alignments by bowtie2
ATAC-seq Bowtie2
5 days ago by Aki ▴ 10
2
votes
4
replies
262
views
Addmetadata to seurat obj
seurat
5 days ago by synat.keam ▴ 100
3
votes
4
replies
330
views
How to download large-scale cDNA sequences from NCBI effectively ?
NCBI. cDNA
updated 2 days ago by 161k • written 3 days ago by ▴ 10
0
votes
4
replies
308
views
What is the samtools flag used in bamPEFragment?
deeptools
updated 5 days ago by 141k • written 7 days ago by • 0
4
votes
4
replies
14k
views
Heatmap with custom gene labels annotated on the rows
differential-gene-expression RNAseq heatmap
updated 6 days ago by 43k • written 4.7 years ago by ▴ 370
1
vote
4
replies
346
views
Is it just me or has www.ensembl.org been broken for a while?
ensembl
4 days ago by gene_biostars • 0
8
votes
4
replies
3.0k
views
Read count correlation between samples
differential-gene-expression RNA-seq
updated 6 days ago by 43k • written 6.5 years ago by ★ 1.6k
0
votes
4
replies
209
views
Downsampling long-read BAM files
nanopore BAM QC ONT downsampling
updated 5 days ago by 141k • written 5 days ago by ▴ 80
0
votes
4
replies
244
views
Adaptive sampling for whole chromosomes
T2T Nanopore AdaptiveSampling aneuploidy centromeres
5 days ago by njornet ▴ 20
8
votes
4
replies
243
views
Ubuntu storage space is decreasing automatically
ubuntu storage
updated 6 days ago by 6.3k • written 6 days ago by ▴ 20
2
votes
4
replies
361
views
Per Base Sequence Content - continuous raise of G%
fastqc
updated 5 days ago by 141k • written 6 days ago by • 0
0
votes
4
replies
805
views
Differential gene expression
limma differential-gene-expression R
updated 6 days ago by 43k • written 4.0 years ago by ▴ 40
0
votes
4
replies
274
views
Questions about transfering wgs file to reference genome file
fasta cram genome
4 days ago by me • 0
0
votes
4
replies
399
views
Gene Ontology question
differential-expression Gene-ontology
updated 6 days ago by 43k • written 15 days ago by • 0
1
vote
4
replies
775
views
I want to calculate if the sample has whole genome duplication event or not?
sequencing wgs
6 days ago by Hyper_Odin ▴ 310
4
votes
4
replies
308
views
How to fetch published paper of a BioProject
BioProject pumbed NGS
6 days ago by Morteza • 0
4
votes
4
replies
337
views
How do I install plink2 on a mac?
plink2 plink
updated 1 day ago by 11k • written 3 days ago by ▴ 10
0
votes
4
replies
1.9k
views
Requesting help with RNA-Seq differential gene analysis
differential-gene-expression deseq2
updated 6 days ago by 43k • written 6.2 years ago by ▴ 50
1
vote
4
replies
359
views
what is the normal range of htseq-count output for homo sapiens RNA-Seq
Transcriptomics htseq-count RNA-Seq NGS hisat2
updated 3 days ago by ★ 1.6k • written 4 days ago by • 0
1
vote
3
replies
3.3k
views
How to calculate Differential Gene expression between samples with replicates
Differential-Gene-Expression RNA-Seq
updated 6 days ago by 43k • written 7.8 years ago by • 0
3
votes
3
replies
607
views
Why are there several gene expression files (for example, miRNA) in TCGA for one case?
Differential-gene-expression TCGA miRNA
updated 6 days ago by 43k • written 5 months ago by ▴ 260
2
votes
3
replies
263
views
Using GPUs in snakemake
Parabricks gpu snakemake slurm
6 days ago by raphael.B ▴ 520
270 results • Page 2 of 6
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Comment: Bioinformatics_where do i start
Answer: Bwa sampe - BGI
Comment: Where to find the homopolymer regions bed file for Hg002 genome?
A: Code golf: detecting homopolymers of length N in the (human) genome
Code golf: detecting homopolymers of length N in the (human) genome
Answer: WGCNA network from Adjacency or TOM matrix
A: What Are The Most Common Stupid Mistakes In Bioinformatics?
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Recent Replies
Comment: Visualization of PROKKA Annotation Result? by Joe 21k
Colin's answer is essentially the right one I believe, but the more immediate consideration is: *what are you actually trying to show?* Mo…
Comment: Bioinformatics_where do i start by Pierre Lindenbaum 161k
https://www.biostars.org/p/9554614/ ; https://www.biostars.org/p/98983 ; https://www.biostars.org/p/9583727/ :https://www.biostars.org/p/4…
Answer: Bwa sampe - BGI by Pierre Lindenbaum 161k
bwa sampe produces unsorted SAM , not BAM. converting SAM to BAM will reduce the size sorting the BAM will reduce the size (you can …
Comment: Where to find the homopolymer regions bed file for Hg002 genome? by Bikram Kumar • 0
Hi! Should I delete the stack exchange post? I didn't know that cross posting is bad. [https://meta.stackoverflow.com/a/425789/5140632][1] …
Answer: Visualization of PROKKA Annotation Result? by colindaven 6.3k
You need a genome browser and you can probably use GBK or gff3 format. Here are some suggestions - I like JBrowse best, Artemis in its …
Comment: Where to find the homopolymer regions bed file for Hg002 genome? by Pierre Lindenbaum 161k
cross-posted https://bioinformatics.stackexchange.com/questions/22401
Comment: Tumour purity and ploidy estimation by bp22 ▴ 60
Hi Llyod98, This issue is still unresolved and I have not been able to find a tool or solution for purity and ploidy estimation when ther…
Comment: Ensembl gene id conversion by ATpoint 81k
Can you add some examples. It is hard to debug textual descriptions.
Answer: Which experiments generate Position Frequency Matrix? by ATpoint 81k
Yes, ChIP-seq or similar methods that assay the DNA binding of a protein. But for a reliable matrix you don't need one or two but many data…
Comment: Statistical Advice Needed for RNAseq Data Analysis by ATpoint 81k
> ensuring it's not merely a product of random chance If your approach of getting DEGs is a proper and sound one (e.g. DESeq2 or limma) th…
Comment: Can I compare kallisto counts from samples with different amount of reads? by ATpoint 81k
Unequal numbers of reads are normal, that is why normalization is needed. If you want to do simple analysis such as number of detected gene…
Comment: Error in edgeR/Deseq2 Analysis by ATpoint 81k
Please ask at https://help.galaxyproject.org/ which is the Galaxy help forum.
Comment: RNAseq 1 control 2 different treatment by matteo.levorato • 0
yes, this is what I did. However, since my treatments are very similar each other, when I check upregulated genes in one treatment, they ar…
Comment: snakemake output directory by 进 • 0
it is right answer
Comment: I am new to single cell analysis. Can RNA velocity (spliced/unspliced) be calcul by Spring • 0
Thank you for the kind guidance!
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