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189 results • Page
3 of 4
Sort: Rank
Rank
Views
Votes
Replies
1
vote
4
replies
249
views
How to sort cd-hit-est cluster file
sort
cd-hit-est
2 days ago by
Mo
▴ 40
1
vote
5
replies
277
views
Enrichment of mitochondrial and ribosomal pathways - an artifact?
Pathway
Mitochondria
Ribosome
scRNA-seq
Enrichment
2 days ago by
omer.shomrat
• 0
13
votes
10
replies
641
views
8 follow
scRNAseq Differential expression analysis
scRNA-seq
Differential-Expression
Seurat
updated 3 days ago by
ATpoint
77k • written 6 days ago by
MVJ
▴ 10
3
votes
4
replies
287
views
Dotplot : how to self-define the range of legend
analysis
seq
RNA
updated 3 days ago by
GenoMax
134k • written 4 days ago by
Xuhao
• 0
0
votes
0
replies
108
views
News:
RADseq data analysis course
RADseq
Phylogenomics
Bioinformatics
Populationgenomics
Stacks
4 days ago by
carlopecoraro2
★ 2.4k
3
votes
2
replies
374
views
How to create structural variants ground truth for alignment of two long-read genome assemblies?
yeast
assembly
structural-variation
SV-callers
4 days ago by
Thomas
▴ 20
0
votes
1
reply
202
views
Merging the filename with tsv files for master file
genomics
updated 2 days ago by
barslmn
★ 1.8k • written 4 days ago by
smrutimayipanda
▴ 20
4
votes
6
replies
363
views
Hisat2 index and alignment question
ubuntu
rna-seq
index
hisat2
updated 1 day ago by
Istvan Albert
98k • written 4 days ago by
Athena
• 0
2
votes
4
replies
343
views
Ties in reranked list
fgsea
GSEA
5 days ago by
Hamza
• 0
1
vote
4
replies
353
views
Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempting To Use CuffDiff
CuffDiff
Bash
Cufflinks
5 days ago by
Y
• 0
0
votes
0
replies
146
views
My rMATS output file is not showing gene symbols and only XLOC gene ID are being shown.
rMATS
rMATS-turbo
5 days ago by
Nipan
• 0
2
votes
4
replies
295
views
Using STAR aligner to build index of hg38
hg38
STAR
alignment
RNAseq
index
4 days ago by
Grace
• 0
0
votes
0
replies
156
views
Convert RNASeq V2 data in cBioPortal having RSEM normalized results to TPM values
bioinformatics
TPM
RNASeqV2
cbioportal
RSEM
updated 5 days ago by
4galaxy77
2.8k • written 5 days ago by
shakyaram079
• 0
0
votes
2
replies
274
views
Modify the code to take most abundant reads from a cluster and process it.
cd-hit-est
clustering
4 days ago by
Mo
▴ 40
1
vote
2
replies
245
views
Understanding TCGA barcodes with dot in the fieldname
tcga
updated 2 days ago by
Zhenyu Zhang
▴ 980 • written 5 days ago by
Tahsin
• 0
0
votes
0
replies
157
views
Compare peaks between clusters in sc-ATAC
Peak-Calling
Epigenome
scATAC-seq
updated 5 days ago by
Ram
40k • written 5 days ago by
Ahmed.waraky
▴ 10
1
vote
3
replies
358
views
How to DESeq2 using miRNA data obtained using TCGAbiolinks
R
TCGAbiolinks
DESeq2
TCGA
updated 5 days ago by
Zhenyu Zhang
▴ 980 • written 8 days ago by
Mo
• 0
0
votes
7
replies
508
views
Highly inflated p-values in GWAS by regenie
regenie
plink
gwas
3 days ago by
cwwong13
▴ 20
1
vote
3
replies
274
views
How to find out what adapters to remove after FastQC of RNAseq data?
Trimmomatic
FastQC
NGS
RNA-seq
3 days ago by
ella
• 0
2
votes
5
replies
340
views
Trimmomatic .jar not included anymore?
trimmomatic
ubuntu
linux
updated 6 days ago by
petebio
▴ 100 • written 6 days ago by
Emily
▴ 30
0
votes
1
reply
184
views
News:
EMBL-EBI virtual course | Introduction to RNA-seq and functional interpretation
RNA-seq
updated 6 days ago by
Ram
40k • written 6 days ago by
Rebecca
• 0
0
votes
4
replies
569
views
Weirdness in annotation (missing allele frequencies)
allele-frequency
gnomad
annovar
updated 4 days ago by
Jeremy Leipzig
21k • written 6 days ago by
Can Abdullah
• 0
1
vote
3
replies
232
views
Finding sequences in unannotated genomes using reference coordinates
consensus
VCF
updated 6 days ago by
Ram
40k • written 6 days ago by
Prangan
▴ 20
0
votes
1
reply
217
views
High amount of intronic/intergenic reads in SMARTer stranded total bulk RNAseq
RNA-seq
DNA
SMARTer
updated 6 days ago by
Ram
40k • written 6 days ago by
Mat
▴ 60
2
votes
5
replies
338
views
How to check RNAseq support for annotated genes?
gene
RNA-seq
annotation
updated 1 day ago by
Michael
53k • written 6 days ago by
BioinfoBee
• 0
0
votes
0
replies
342
views
Why dbConnect GEOmetadb_demo.sqlite shows some information while dbConnect GEOmetadb.sqlite shows no information
R
GEO
GEOmetadb
updated 6 days ago by
Pierre Lindenbaum
157k • written 6 days ago by
nonaddldy
▴ 10
1
vote
0
replies
165
views
News:
Online Training - Bioinformatics Pipeline Development with Nextflow (November 15-17, 2023)
nextflow
automation
pipeline
development
6 days ago by
David Langenberger
10k
1
vote
5
replies
359
views
ATAC-seq troubleshoot - Just Noise
ATAC-seq
updated 2 days ago by
ATpoint
77k • written 6 days ago by
vk
▴ 40
2
votes
2
replies
245
views
Simulate short-read RNA-seq data from long-read RNA-seq data
polyester
single-cell
simulation
short-read
long-read
2 days ago by
rhonddaskl
• 0
4
votes
4
replies
423
views
DESeq2 analysis using two featureCounts generated from different studies
RNA-seq
DESeq2
6 days ago by
abedkurdi10
▴ 190
4
votes
4
replies
355
views
Filtering VCF to divide with equal sizes
bcftools
vcf
updated 6 days ago by
Ram
40k • written 7 days ago by
avelarbio46
▴ 30
0
votes
0
replies
173
views
High pvalues when using clusterProfiler for seurat
clusterProfiler
6 days ago by
Ahmed
• 0
5
votes
2
replies
250
views
kallisto normalized TPM values without bootstraps
tpm
cibersort
sleuth
kallisto
RNA-seq
6 days ago by
butterman16
▴ 20
5
votes
7
replies
424
views
Salmon index not progressing
salmon
updated 6 days ago by
Michael
53k • written 6 days ago by
camillab.
▴ 140
0
votes
0
replies
166
views
scanpy problem for empty cells
scanpy
updated 6 days ago by
Ram
40k • written 6 days ago by
Andy
▴ 90
0
votes
0
replies
170
views
Current landscape of approaches to scRNA-seq with nanopore sequencers?
scRNA-seq
nanopore
single-cell
4 days ago by
LauferVA
3.7k
0
votes
1
reply
211
views
How to download genomes and proteins from JGI in bulk via the command line?
jgi
cli
updated 6 days ago by
Ram
40k • written 6 days ago by
O.rka
▴ 680
2
votes
1
reply
220
views
News:
Successful NCBI NIAID Codeathon on VCF Files in SARS-CoV-2 Genomics
NCBI
Codeathon
updated 4 days ago by
chrchang523
10k • written 7 days ago by
PeterC_NCBI
▴ 330
3
votes
4
replies
394
views
Chromosome bias on RNA-Seq differential gene expression analysis
chromosome-bias
RNA-seq
6 days ago by
blz
▴ 30
0
votes
5
replies
449
views
genome data downloads for various strains
gisaid
hass-marr
updated 3 days ago by
Ram
40k • written 7 days ago by
iftikharmaryam123
• 0
4
votes
8
replies
581
views
Assistance with Fungal Genome Annotation Using Maker and BLAST
gff3
fasta
maker
xml
blastp
3 days ago by
Edoardo
• 0
3
votes
10
replies
512
views
STAR index not working
STAR
RNA-Seq
6 days ago by
camillab.
▴ 140
0
votes
13
replies
577
views
STAR Intron Motif Script Gives Segmentation fault Error
STAR
Linux
5 days ago by
Y
• 0
0
votes
13
replies
683
views
Dealing with transcriptome sequences that are smaller than their respective genes
blastn
Trinity
Transcriptome
RNA-seq-analysis
De-novo-transcriptome-assembly
6 days ago by
langziv
▴ 50
10
votes
8
replies
590
views
Adding a control sample to bulk RNA-seq
RNA-seq
6 days ago by
Chris
▴ 200
6
votes
8
replies
536
views
Find potential important genes from bulk-RNA seq experiment
RNA-seq
5 days ago by
Chris
▴ 200
6
votes
1
reply
170
views
How to retrieve sample informations from given ID from Sequence Read Archives?
eutils
SRA
updated 2 days ago by
Ram
40k • written 9 days ago by
DareDevil
★ 3.3k
2
votes
8
replies
484
views
Read block operation failed with BAM file
bgzip
samtools
bam
pysam
htslib
updated 2 days ago by
John Marshall
3.0k • written 10 days ago by
Alex Reynolds
35k
3
votes
2
replies
281
views
Scanning for ultra-hot topics in science via pubmed, or using other tools
growth
pubmed
6 days ago by
LauferVA
3.7k
15
votes
6
replies
1.0k
views
Annotating TSS: By Transcript or by Gene? Code Validation Help Needed!
genome
bed
transcript
TSS
2 days ago by
Rafael Soler
★ 1.2k
189 results • Page
3 of 4
Recent Votes
C: How Do I Convert Fa Files To Bed Format?
Clustering in single cell
Answer: Network analysis with cytoscape
Answer: Network analysis with cytoscape
Network analysis with cytoscape
Comment: How to convert data in r?
Comment: Frustrated with DEA results
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Recent Replies
Comment: Github access with token headache
by
Ram
40k
Yes please.
Comment: How to convert data in r?
by
Ram
40k
> tidyr does not make anything tidy at all I don't get your point. The code does not use tidyr (`%>%` is from `magrittr`) and there is no …
Comment: Unmapped Reads in Kallisto
by
GenoMax
134k
https://www.biostars.org/u/30020/ you can add a solution to this thread. It looks like this poster has a similar issue described in origina…
Comment: Unmapped Reads in Kallisto
by
dsull
★ 4.7k
Create a new thread if you need help with this.
Comment: Network analysis with cytoscape
by
Chris
▴ 200
Thanks xanderpico! That is great resources. There are many bioinformatics tools now which is hard to choose an appropriate one. I found thi…
Comment: Frustrated with DEA results
by
dsull
★ 4.7k
Great suggestion on visualizing the data as well as doing DE between variables that you know should result in different gene expression pro…
Answer: Network analysis with cytoscape
by
xanderpico
▴ 500
Hi Chris. There are dozens of different directions you could go using Cytoscape. There is not just one analysis path. You mention "tran…
Comment: How to convert data in r?
by
Jeremy
▴ 840
Great answer bk11. star, you'll need the dplyr package to run this code. Just make the following the first line of code: library(dpl…
Comment: Troubles launch IGV on Linux(Debian)
by
PoscaXVIII
• 0
Hi barslmn, Thank you so much for your help it works perfectly. No more frozen black screen. I just changed from wayland to Xorg (On the pa…
Comment: Complex multifactorial DE analysis with limma/edgeR based on rnaseq data
by
LChart
3.4k
> I tried a general "overall" group comparison of the "general" conditions, trying to model the "donor" effect and including it into the de…
Comment: How to convert data in r?
by
Kevin Blighe
86k
Funny how *tidyr* does not make anything tidy at all. Why not just use (actually less characters): data <- data.frame(c( "A \t 22…
Comment: Frustrated with DEA results
by
Jeremy Leipzig
21k
If the FDR is killing your results, it's ok to filter out genes that are not informative https://www.bioconductor.org/help/course-materials…
Comment: Github access with token headache
by
Begonia_pavonina
▴ 110
I will post it in StackOverflow, should I delete this thread?
Comment: How to convert data in r?
by
bk11
★ 1.2k
Hope OP will add biological context to this query and answering- data <- c( "A \t 2212 \t 2267 \t 2299", " \t 2015 \t 2068…
Comment: Github access with token headache
by
Ram
40k
This post does not fit the theme of this forum. Just because you're trying to upload a bioinformatics pipeline does not mean this needs bio…
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