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122,017 results • Page 593 of 2441
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1
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0
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866
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Fisher exact test for transcription factor binding motif enrichment analysis
motif p-value denovo R
4.1 years ago by Rana Rehan ▴ 10
0
votes
1
reply
4.1k
views
haplotype network analysis with Pegas package in R
haplotype pegas R
updated 4.1 years ago by ▴ 40 • written 5.5 years ago by ▴ 200
8
votes
6
replies
2.1k
views
bash script
info snp model substring
updated 4.1 years ago by 45k • written 4.1 years ago by ▴ 20
2
votes
2
replies
1.4k
views
Forum: Internship in research
python genomics
4.1 years ago by vaishnavi ▴ 80
0
votes
0
replies
1.5k
views
A USER ERROR has occurred: no positional argument is defined for this tool.
GATK4 HaplotypeCaller BAM
updated 4.1 years ago by 45k • written 4.1 years ago by ▴ 60
4
votes
1
reply
1.4k
views
adjusting for confounding factors in Spearman correlation?
sapply spearman r
updated 4.1 years ago by ★ 3.1k • written 4.1 years ago by ▴ 20
4
votes
2
replies
1.2k
views
What aa should I use in 2nd structure prediction instead of X
structure protein prediction
4.1 years ago by Xylanaser ▴ 80
3
votes
3
replies
1.3k
views
problem in y axis in barplot+ggplot
barplot ggplot
4.1 years ago by hasani.iut6 ▴ 60
2
votes
0
replies
908
views
Precomputed TCGA MC3 tumor purity data
TCGA
4.1 years ago by Yu ▴ 140
1
vote
2
replies
1.3k
views
Single-cell RNA Seq on whole organ or whole tissue with known cell origins
known-cell-origin whole-organ single-cell-RNA-Seq whole-tissue
4.1 years ago by zhang.jianhai ▴ 30
0
votes
0
replies
1.0k
views
Job: Postdoctoral Scientist in Statistical Bioinformatics, WEHI, Melbourne, Australia
australia
4.2 years ago by Gordon Smyth ★ 8.3k
0
votes
0
replies
591
views
merging the co-expression networks from different tissue in one disease
RNA-seq networks expression Merging
4.2 years ago by sheikhbeigali • 0
1
vote
1
reply
1.1k
views
FreeBayes Error
Galaxy Coursera FreeBayes Polymorphisms
updated 4.1 years ago by ▴ 580 • written 4.2 years ago by • 0
0
votes
2
replies
1.8k
views
Removal of host sequences without reference genome
meta-genomic contaminants missing host reference genome viral
4.2 years ago by emiliomastriani ▴ 40
0
votes
0
replies
1.4k
views
REditools2 (HPC-reditools) de-novo editing prediction from RNAseq?
editing reditools2 prediction RNAseq
4.2 years ago by RNAseqer ▴ 280
1
vote
2
replies
4.1k
views
FindMarkers for ClusterProfiler
ClusterProfiler gseGO enrichGO
4.1 years ago by cgp09741 ▴ 10
0
votes
5
replies
2.9k
views
PLINK --lasso Issue ('Warning: No Phenotypes Present') even with a covar file is present
PLINK
updated 2.6 years ago by 45k • written 4.2 years ago by • 0
2
votes
3
replies
6.8k
views
Seurat re-clustering a cell subset but cell identity numbers are not completely showing up
scRNA
4.1 years ago by leranwangcs ▴ 150
0
votes
0
replies
647
views
snsplot in Rshiny through images using reticulate
renderImage reticulate rshiny R
4.2 years ago by vinishavvenugopal ▴ 30
1
vote
3
replies
2.0k
views
Validation of somatic variant calling pipeline
calling somatic validation variant
updated 4.2 years ago by 23k • written 4.2 years ago by • 0
1
vote
1
reply
953
views
BSgenomes for HIV viruses
CLIP-seq RNA-Seq CLIP-Seq
updated 4.1 years ago by 89k • written 4.2 years ago by ▴ 140
0
votes
0
replies
655
views
Network MJ mitochondrial SNPs
mitochondrial SNPs network Median-joining
4.2 years ago by pmc.sa ▴ 40
3
votes
1
reply
1.1k
views
Build protein-protein interaction prediction deep learning model
interaction machine learning deep protein-protein
updated 4.2 years ago by ★ 30k • written 4.2 years ago by ▴ 20
0
votes
0
replies
600
views
TCGA Agilent level 2 to level 3
TCGA
4.2 years ago by rebeliscu ▴ 60
0
votes
4
replies
1.7k
views
batch correction in ChIp-seq data
batch ChIP-seq
updated 4.1 years ago by 13k • written 4.2 years ago by ★ 1.4k
0
votes
1
reply
1.5k
views
Gdcprepare() error.
Gdcprepare
updated 4.1 years ago by 45k • written 4.2 years ago by • 0
2
votes
4
replies
1.6k
views
Need suggestions about pathogenicity prediction of gdc level 3 SNV file
gdc TCGA SNVs
4.1 years ago by SUMIT ▴ 30
0
votes
0
replies
664
views
Computing Recombination rate
recombination rate
4.2 years ago by elhamidihay ▴ 30
1
vote
8
replies
4.7k
views
Problem merging data in plink
Plink
4.2 years ago by Max ▴ 10
0
votes
0
replies
779
views
how to demultiplex scRNAseq fastq with barcode in read2
demultiplex fastq
4.2 years ago by Binghong ▴ 20
0
votes
0
replies
1.1k
views
Job: Assistant Professor (tenure-track) and Professor positions in Data Science
data-science statistics faculty
updated 2.6 years ago by 45k • written 4.2 years ago by ▴ 10
1
vote
2
replies
1.4k
views
What is the best software for "phasing" in human population genomics with trio family pedigree?
Trio Phasing genomics pedigree SNP
updated 4.2 years ago by ▴ 900 • written 4.2 years ago by ▴ 10
0
votes
0
replies
870
views
Job: Jr and Sr bioinformatician profiles for immunotherapy design in cancer patients (BELGIUM)
neoantigen belgium
updated 2.3 years ago by 45k • written 4.2 years ago by • 0
2
votes
8
replies
4.9k
views
Gene read count-level batch correction in scRNA-seq?
RNA-seq NGS single-cell-sequencing
updated 2.4 years ago by 13k • written 4.2 years ago by ▴ 10
1
vote
1
reply
909
views
input to Trimmomatic tool
to Trimmomatic input
updated 4.2 years ago by 154k • written 4.2 years ago by ▴ 10
1
vote
1
reply
978
views
Extract batch variable from GEO dataset
GEO batch_analysis microarray
updated 4.2 years ago by 89k • written 4.2 years ago by ▴ 250
3
votes
4
replies
1.8k
views
Gene co-expression in single-cell RNA-seq
single-cell scRNA-seq RNA-seq correlation co-expression
updated 4.2 years ago by 13k • written 4.2 years ago by ▴ 100
9
votes
6
replies
5.4k
views
From amino acid sequence to DNA sequence using Reverse Translate software
DNA translation protein coordinate-mapping
4.2 years ago by Student ▴ 30
0
votes
0
replies
554
views
Looking for a lncRNA seq dataset for Acute Lymphoblastic Leukemia
Leukemia RAN_seq lncRNA Acute Lymphoblastic
4.2 years ago by MRezaei ▴ 40
4
votes
2
replies
2.6k
views
[HuGene-1_0-st] Affymetrix Human Gene 1.0 ST Array [transcript (gene) version], hugene10sttranscriptcluster.db, AnnotationDbi
AnnotationDbi hugene10sttranscriptcluster.db
4.2 years ago by appropiate ▴ 80
0
votes
2
replies
2.2k
views
Is there a way to separate the chains belong to each Biological assembly in a PDB file?
python biopython
updated 2.6 years ago by 45k • written 5.9 years ago by • 0
0
votes
4
replies
2.2k
views
UMAP of TRA/B
seurat r
updated 4.2 years ago by 13k • written 4.2 years ago by • 0
0
votes
0
replies
772
views
Any online tools to do in silico RE digestion for unmapped nanopore sequencing reads?
nanopore sequencing
updated 4.2 years ago by 45k • written 4.2 years ago by • 0
1
vote
3
replies
1.2k
views
finding functional rare and synonymous alleles in a vcf file
exome variants
updated 4.2 years ago by 45k • written 4.2 years ago by ▴ 30
0
votes
1
reply
1.2k
views
Sequence search parameters for annotation of de novo transcriptomes
annotation transcriptome search blast
updated 4.2 years ago by 5.3k • written 4.2 years ago by ★ 2.9k
4
votes
6
replies
2.4k
views
6 follow
DESeq2 rlog-transformed RNA-seq data for machine learning input
rlog deeplearning DESeq2 machinelearning
updated 4.1 years ago by 89k • written 4.2 years ago by ▴ 20
2
votes
5
replies
1.7k
views
Spatial analysis with colocalization
colocalization programming imaging
updated 4.2 years ago by ★ 30k • written 4.2 years ago by ▴ 20
2
votes
3
replies
1.9k
views
GDC RNA-seq pipeline: Original vs. Dr15plus?
RNA-seq GDC
updated 4.1 years ago by ★ 1.3k • written 4.2 years ago by ▴ 60
0
votes
6
replies
1.5k
views
To find total genes on favorable chromosome
genes total
updated 4.2 years ago by 89k • written 4.2 years ago by • 0
41
votes
7
replies
3.8k
views
9 follow
linux for genomics
linux genomics
updated 4.2 years ago by ▴ 310 • written 4.2 years ago by ▴ 80
122,017 results • Page 593 of 2441
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Answer: 1 vs 1 DEG analysis in scrna seq data
A: Bam And Indexed Bam Files
BCFtools consensus sequence
A: Bam And Indexed Bam Files
Answer: How to create a phylogenetic tree from 30 VCF files
Comment: Reading AD and other genotype information from the VCF file
Answer: 1 vs 1 DEG analysis in scrna seq data
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Recent Replies
Comment: Quantification using salmon in alignment-based mode after minimap2 run by Assa Yeroslaviz ★ 1.9k
Hi Rob, sorry for the late question. I was wondering though, if I can also quantify transposable elements using oarfish? Should I increas…
Answer: 1 vs 1 DEG analysis in scrna seq data by ATpoint 89k
The only option you have is to treat every single cell as a replicate. That has the obvious downside that any effect can be a donor-unique …
Answer: GUI commercial software for 10x single cell gene expression analysis by firestar ★ 1.7k
An open-source option: [kana](https://www.kanaverse.org/kana/).
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Edward • 0
Yes, we plan to make English the primary language of the Brave UI.
Comment: Reasonable number of SNPs in a bacterial genome. by michael.ante ★ 4.0k
If your bacterial species is a (human) pathogen, you might want to check outbreak analysis papers of that species. In general, you find t…
Comment: hisat2 error-Paired end reads not equal or lack of RAM/disk space? by lieven.sterck 16k
ok, missed that ... in any case that should not happen indeed. How did you determine that the files are not equal? I can indeed also see t…
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Ram 45k
Do you have a plan to make an English version of the UI?
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by Edward • 0
This can visualize the parameters of the generated workflow, software, and scripts, and manage the docker process of the script, software, …
Comment: Brave: Bioinformatics Reactive Analysis and Visualization Engine by ATpoint 89k
Can you summarize in one sentence what the use case is? Is this a workflow manager?
Comment: Pseudogene - scarce info by ATpoint 89k
This reminds me strongly on my "masters" courses (doesn't deserve that name tbf). "Here is some poorly-described project with little to no …
Answer: scVI vs Harmony, which is better for cell type based clustering in brain tissue? by ATpoint 89k
There is no "better" is my experience. It always depends on the dataset. Try both and integrate your biological knowledge to decide which m…
Comment: DESeq2 on metagenome KO counts by Aleksandra ▴ 190
I just wrote that I misunderstood your initial question.
Comment: DESeq2 on metagenome KO counts by Aleksandra ▴ 190
What exactly did I not get?
Comment: Interpreting genomic features distribution for CUT&RUN peaks by rfran010 ★ 1.7k
If I understand correctly, you see increased signal at TSS sites compared to control (taller peaks in browser). However, 92% of the 450 siS…
Comment: combine VCF from diploid reference/haplotypes for the same sample by cmdcolin ★ 4.3k
this question is a little similar to your previous question (https://www.biostars.org/p/9614638/). just as added info, here is a tool calle…
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