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1,000 results • Page 5 of 20
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0
votes
3
replies
265
views
Software to separate reads from different individuals
software development nanopore
updated 20 days ago by 142k • written 20 days ago by ▴ 20
0
votes
2
replies
376
views
How to update R on ubuntu
installation update R apt-get
20 days ago by Bosberg ▴ 50
0
votes
0
replies
130
views
LEfSe
LEfSe
20 days ago by benkosta • 0
0
votes
0
replies
107
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq DEXSeqDataSet SGSeq
20 days ago by Sara ▴ 30
0
votes
2
replies
205
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression DEG model
20 days ago by Lluís R. ★ 1.2k
0
votes
0
replies
127
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics Mass-spectrometry Proteins
updated 6 days ago by 43k • written 20 days ago by ▴ 40
0
votes
2
replies
250
views
What should I consider as FASTA for dataset?
PDB FASTA
20 days ago by Nafi • 0
0
votes
0
replies
612
views
Differential accessibility using DiffBinf
diffbind
21 days ago by Shloka • 0
0
votes
0
replies
119
views
vg call vs vg surject
vg variation graphs
updated 20 days ago by 142k • written 21 days ago by • 0
0
votes
1
reply
246
views
Finding batch and outlayers
Pca
updated 20 days ago by ▴ 460 • written 21 days ago by • 0
2
votes
2
replies
249
views
PDB related issue
rcsb pdb
updated 21 days ago by ▴ 580 • written 21 days ago by • 0
0
votes
9
replies
2.6k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome base-calling fastq nanopore
updated 21 days ago by 43k • written 9 months ago by • 0
1
vote
2
replies
288
views
Downloading full alignments from Pfam
pfam
14 days ago by bef1 • 0
0
votes
0
replies
142
views
adjusting for confounders in LMER in R
confounders LMER R
updated 20 days ago by 14k • written 21 days ago by ▴ 20
1
vote
3
replies
385
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 21 days ago by 82k • written 22 days ago by ▴ 10
0
votes
0
replies
159
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
22 days ago by tnminh89 ▴ 10
0
votes
0
replies
160
views
Filter low express genes in microarray data
microarray
22 days ago by Chris ▴ 280
0
votes
0
replies
588
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell Spatial-Transcriptomics
23 days ago by biocellbio • 0
0
votes
0
replies
226
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes vcf phasing
23 days ago by HarperReed • 0
1
vote
0
replies
176
views
Simulation of label-free bottom-up proteomics expression dataset
label-free bottom-up lc-ms proteomics
23 days ago by KABILAN ▴ 70
0
votes
0
replies
192
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics phylogenetic
updated 23 days ago by 43k • written 24 days ago by • 0
0
votes
0
replies
192
views
RNA-seq: full length gene
RNA-seq
updated 23 days ago by 43k • written 24 days ago by • 0
0
votes
0
replies
173
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly phased Haplotype Annotation
24 days ago by turcoa1 • 0
0
votes
0
replies
186
views
Designing single-stable RNA molecules
structure RNA
24 days ago by Edna • 0
0
votes
0
replies
198
views
How to visualize/predict the final transcript from Delly output?
WGS DELLY
24 days ago by simplitia ▴ 130
1
vote
1
reply
271
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing housekeeping Single-cell normalization
updated 24 days ago by 82k • written 24 days ago by • 0
0
votes
0
replies
183
views
How to calculate correlation coefficient for chipseq?
chipseq bigwigsummary deeptools correlation
6 days ago by Emily ▴ 20
1
vote
0
replies
197
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds kaks VCF
24 days ago by rohitsatyam102 ▴ 870
0
votes
0
replies
174
views
how to read graph_test output of monocle 3
monocle3
24 days ago by synat.keam ▴ 100
0
votes
1
reply
538
views
GAPIT p-value significance threshold
GAPIT p-value GWAS
updated 24 days ago by • 0 • written 5 months ago by • 0
0
votes
0
replies
179
views
Why not use iBAQ for calculating differential abundance of proteins?
protein maxquant
24 days ago by Aspire ▴ 330
0
votes
4
replies
428
views
Highest variable features in single cell data
single-cell
12 days ago by carolofharvest ▴ 40
1
vote
3
replies
456
views
PCA plot
DESeq2 PCAplot
updated 21 days ago by 4.2k • written 25 days ago by ▴ 10
0
votes
0
replies
176
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein pdb alpha-carbon
25 days ago by 4fzcgueyp5 • 0
0
votes
2
replies
315
views
Annovar using R package
Annovar gnomAD R
24 days ago by DKA ▴ 40
0
votes
5
replies
446
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative ncbi asembly refseq
updated 24 days ago by 142k • written 25 days ago by ▴ 90
0
votes
0
replies
172
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA GDCprepare
updated 25 days ago by 43k • written 25 days ago by • 0
0
votes
0
replies
331
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome PGAP NCBI roary Prokka
25 days ago by pramach1 ▴ 40
0
votes
1
reply
212
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate GEMMA GWAS
updated 25 days ago by • 0 • written 25 days ago by • 0
0
votes
0
replies
170
views
Sequence BLAST in plus/minus and plus/plus
blast CRISPR strand sequencing
25 days ago by salias • 0
0
votes
5
replies
469
views
different FeatureCounts output for the same data
fpkm Counts Rsubread rna-seq
updated 22 days ago by 100k • written 25 days ago by ▴ 10
0
votes
0
replies
147
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq single-cell suppa alternative-splicing
updated 25 days ago by 43k • written 25 days ago by • 0
1
vote
2
replies
284
views
alignment result
RNA-seq samtools hisat2
25 days ago by ahmad.sajad4541 • 0
0
votes
0
replies
141
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile scvelo scipy annData numpy
26 days ago by Kash ▴ 110
0
votes
1
reply
194
views
How to solve this RoseTTAFold colaboratory error?
modeling Google Colaboratory RoseTTAFold protein
updated 26 days ago by ★ 27k • written 26 days ago by • 0
2
votes
2
replies
339
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein FASTA alignment
updated 25 days ago by 43k • written 26 days ago by ▴ 140
2
votes
9
replies
947
views
TCGA2STAT Error: Firehose connection
FIREHOSE TCGA
updated 26 days ago by 4.2k • written 7 months ago by • 0
0
votes
11
replies
725
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo scRNA-seq STAR snRNA-seq MGI
24 days ago by atowns21 • 0
0
votes
1
reply
217
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering subclustering scRNAseq
updated 26 days ago by ★ 2.5k • written 26 days ago by • 0
0
votes
0
replies
124
views
The concept of co-occurrence network structure
co-occurence microbiome network
26 days ago by ohtang7 ▴ 40
1,000 results • Page 5 of 20
Recent Votes
Answer: How to find tandem duplications pattern in a DNA sequence
A: How To Split One Big Sequence File Into Multiple Files With Less Than 1000 Seque
C: Snakemake vs. Nextflow: strengths and weaknesses
Answer: workflow management system : WDL, CWL, Ruffus, SnakeMake, etc
Sequence alignment on split read event such as inversion, duplication and complex nested events.
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
Comment: Add stats to the plot
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Recent Awards • All
Scholar to Pierre Lindenbaum 161k
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Recent Replies
Comment: Add stats to the plot by marco.barr ▴ 130
The error is likely due to the fact that the structure of your data in data4.ts and data2.ts may not contain the Condition values. The grou…
Comment: How to find identical sequences in genome fasta file (by Python or any possible by Pierre Lindenbaum 161k
+ https://www.biostars.org/p/3003/ + https://www.biostars.org/p/9550118/ + https://www.biostars.org/p/158148/
Answer: How to find tandem duplications pattern in a DNA sequence by micah ▴ 30
I built a web application can directly find repeat unit and repeat times, try it at http://64.64.240.35:8050/. ![Dot plot][1] ![5 tandem …
Comment: What marks a De-Novo Genome assembly as FAILED? by nd48 ▴ 20
I would urge you to consider different approaches for benchmarking before deciding on one. In particular, I found that assembling long read…
Comment: BiomartException: Query ERROR for existing dataset in BioMart by Luqman • 0
I am using *pybiomart* which has Server inplace of BiomartServer, I used that as per above but still getting the same error. Also, when I a…
Comment: Blastn, need help to increase speed by m13113153781 • 0
mmseq2 is indeed a good acceleration solution, but its index files require ~ 6 T space....
Answer: seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from by KHURRAM SHAHZAD • 0
Thank you it works
Answer: Add stats to the plot by Ghada • 0
I think this is what caused the error. we do not have group 1 and 2 in the statistical test results???? ![enter image description here][…
Answer: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data? by Bibi • 0
@atpoint thanks you for your timely response. Can someone else shed light if we can compare the trend of DEGs using the scRNA and Bulk RNA…
Comment: Add stats to the plot by GenoMax 142k
Please use `101010` to format `code` so it is represented in monospace font. I have done this for you now.
Answer: is there a tool to recover corrupted fastq files by Tommaso • 0
You may also want to give a try to **FastqWiper** (https://github.com/mazzalab/fastqwiper)
Comment: Add stats to the plot by Ghada • 0
Thanks. That helpful. I am getting this error data4_test <- data4.ts%>% ungroup() %>% t.test(data =.,value ~ Condition)%>% + …
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data? by ATpoint 82k
I cannot comment here. You are asking why results between two experiments are different. I do not know without seeing the data.
Comment: scRNA-seq data trained model can be used for predictions on bulk RNA-seq data? by Bibi • 0
Thank you so much for this insight. I just want to clarify another point here. I have used scRNA seq data from mice mammary epithelial cell…
Comment: Is it Possible to "Merge" data from Replicates within a VCF SNP File by Pierre Lindenbaum 161k
> Cannot read non-existent file: file:///local/home/User/VCF_Filtering/biostar.code your file doesn't exist, is at the wrong place etc.
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