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43 results • Page
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84
votes
47
replies
30k
views
28 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 23 hours ago by
Ram
40k • written 10.0 years ago by
Irsan
★ 7.7k
100
votes
38
replies
29k
views
34 follow
Forum:
List of cloud genomics companies
cloud-genomics
updated 1 hour ago by
Jeremy Leipzig
21k • written 9.9 years ago by
14134125465346445
★ 3.6k
100
votes
33
replies
105k
views
23 follow
How To Split A Bam File By Chromosome
bam
split
chromosome
updated 6 hours ago by
ella
• 0 • written 11.3 years ago by
GPR
▴ 390
13
votes
16
replies
630
views
ncbi error report log for validate fastq issue
sra-tools
updated 23 hours ago by
GenoMax
134k • written 1 day ago by
1769mkc
★ 1.1k
3
votes
12
replies
230
views
How to subset large BAM files specifically/ extract specific subsets?
bamtools
RNAseq
samtools
BAM
updated 2 hours ago by
GenoMax
134k • written 6 hours ago by
ella
• 0
13
votes
12
replies
32k
views
Estimating Insert Size From Paired End Data.
picard
alignment
paired-end
updated 23 hours ago by
Ram
40k • written 9.6 years ago by
GouthamAtla
12k
1
vote
6
replies
233
views
Github access with token headache
Github
git
offtopic
2 hours ago by
Begonia_pavonina
▴ 110
0
votes
6
replies
279
views
Troubles launch IGV on Linux(Debian)
IGV
1 hour ago by
PoscaXVIII
• 0
0
votes
6
replies
327
views
Bacterial Pangenome Analysis
Prokka
Pangenome
bacteria
Roary
10 hours ago by
kirankumareripogu
▴ 10
4
votes
5
replies
270
views
identify DEGs across all conditions and per specific conditions
R
DEseq2
4 hours ago by
camillab.
▴ 140
1
vote
5
replies
183
views
CollectRnaSeqMetrics (Picard) output to convert FeatureCounts into TPM
R
Picard
CollectRnaSeqMetrics
updated 2 hours ago by
Ram
40k • written 1 day ago by
camillab.
▴ 140
2
votes
5
replies
163
views
Frustrated with DEA results
microarray
differential-expression
updated 30 minutes ago by
dsull
★ 4.7k • written 1 day ago by
jopadrosa
• 0
4
votes
5
replies
904
views
6 follow
Apple Silicon M1 for sequencing and base calling in MinION Mk1B Oxford Nanopore Sequencer
MinION
Oxford-Nanopore
updated 21 hours ago by
GenoMax
134k • written 5 months ago by
satrio
▴ 10
4
votes
5
replies
1.9k
views
ChIP-seq heatmap input bed file
bed
chip-seq
deeptools
heatmap
updated 9 hours ago by
Miao Zhang
• 0 • written 23 months ago by
buffealo
▴ 90
1
vote
5
replies
128
views
6 follow
How to convert data in r?
R
offtopic
updated 1 hour ago by
Jeremy
▴ 840 • written 3 hours ago by
star
▴ 350
1
vote
5
replies
317
views
Number of accessible regions included by DESeq2 to generate the PCA plot with the nf-core ATACseq pipeline ?
nf-core
atac-seq
PCA
DESeq2
updated 2 hours ago by
Michael Love
★ 2.5k • written 1 day ago by
Alexandre Eeckhoutte
• 0
2
votes
5
replies
209
views
Mapping SNP rsIds/ positions to genes coding for proteins
SNP
rsid
5 hours ago by
Harsh
• 0
2
votes
4
replies
255
views
Which function is best for pathway analysis?
pathway
20 hours ago by
Chris
▴ 200
2
votes
4
replies
3.7k
views
Is there a way to use CNVkit without a reference from normal samples?
sequence
CNVkit
updated 4 hours ago by
Matteo Schiavinato
★ 3.6k • written 5.5 years ago by
leandro.bispo.oliveira
• 0
3
votes
4
replies
148
views
Network analysis with cytoscape
RNA-seq
cytoscape
just now by
Chris
▴ 200
0
votes
4
replies
132
views
Software tool to filter productive sequences
protein
fasta
updated 2 hours ago by
Ram
40k • written 6 hours ago by
sperezilvia
▴ 10
1
vote
3
replies
176
views
Chip-Seq and correlation of bam file
Chip-Seq
updated 2 hours ago by
jared.andrews07
★ 15k • written 1 day ago by
qudrat.nii
• 0
0
votes
3
replies
173
views
Complex multifactorial DE analysis with limma/edgeR based on rnaseq data
R
edgeR
limma
RNA-seq
updated 1 hour ago by
LChart
3.4k • written 22 hours ago by
svlachavas
▴ 780
1
vote
3
replies
294
views
How to determine the total count for each gene in lymphotype B
scRNAseq
Seurat
5 hours ago by
dalibenam64
• 0
0
votes
3
replies
1.1k
views
Unmapped Reads in Kallisto
Kallisto
RNA-Seq
alignment
bustools
updated 26 minutes ago by
GenoMax
134k • written 3.6 years ago by
msutennis23
• 0
3
votes
3
replies
164
views
Have some issues in running prokka on WSL
prokka
updated 2 hours ago by
Ram
40k • written 19 hours ago by
Kirill
▴ 10
0
votes
2
replies
127
views
Splitting VCF/BCF file into seperate gene files
genomics
bcftools
eqtl
gwas
updated 11 hours ago by
Pierre Lindenbaum
157k • written 16 hours ago by
Lynne-95
• 0
0
votes
2
replies
191
views
ptt and rnt files that were created from assembly rather than a genome
rockhopper
genbank
12 hours ago by
langziv
▴ 50
0
votes
2
replies
147
views
Detect STRs in illumina library
repeats
annotation
STR
12 hours ago by
kirillkirilenko
▴ 20
0
votes
2
replies
491
views
RSEM not giving .genes.results and isoforms.results ; Plase check if you provide correct parameters/options for the pipeline!
genomics
transcriptome
rsem
ngs
11 hours ago by
kat.bi
• 0
1
vote
2
replies
377
views
The bam file used for DiffBind?
DiffBind
ATAC-seq
9 hours ago by
Miao Zhang
• 0
2
votes
2
replies
140
views
Get support value of MRCA given a list of tip.label in R newick trees
phylogeny
newick
R
ape
tree
5 hours ago by
pl.terzian
• 0
0
votes
2
replies
1.2k
views
Converting hdf5 file to loom file
single-cell
python
scvelo
RNA
updated 3 hours ago by
bk11
★ 1.2k • written 2.4 years ago by
sidrah.maryam
▴ 50
1
vote
2
replies
94
views
Allele frequency calculation for genotype dosage value
plink
dosage
r
impute
3 hours ago by
Sebastian
• 0
1
vote
2
replies
136
views
comparision of umap single cell
single-cell
updated 2 hours ago by
Ram
40k • written 17 hours ago by
synat.keam
▴ 80
1
vote
1
reply
105
views
Transcription factor co-localization p-values
p-values
updated 19 hours ago by
jared.andrews07
★ 15k • written 22 hours ago by
Vishal
▴ 10
0
votes
0
replies
45
views
Software for chimera detection of amplicon (e.g. 16S) nanopore reads
chimera
nanopore
amplicon
8 hours ago by
rob_DNA
▴ 10
0
votes
0
replies
11
views
Convert from limma voom normalized matrix each gene to high/low
RNA-SEQ
voom
limma
OS
survival
1 hour ago by
Manuel Sokolov Ravasqueira
▴ 100
1
vote
0
replies
18
views
Clustering in single cell
seurat
single-cell
49 minutes ago by
Chris
▴ 200
0
votes
0
replies
60
views
Assessing Rockhopper's output
transcriptome
Rockhopper
RNA-seq
de-novo-assembly
12 hours ago by
langziv
▴ 50
0
votes
0
replies
59
views
tensorQTL interaction issue
genomics
eqtl
genetics
qtl
18 hours ago by
Solal
• 0
0
votes
0
replies
45
views
Guide for ICD-10 to EFO conversion?
icd10
efo
7 hours ago by
optimistsso4co3
▴ 100
0
votes
0
replies
1
view
Issue with merging in plink and eigensoft.
Eigensoft
Eigenstrat
Plink
just now by
Jd
• 0
43 results • Page
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Recent Votes
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
Answer: Allele frequency calculation for genotype dosage value
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Recent Replies
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…
Comment: Frustrated with DEA results
by
colindaven
5.5k
There are good answers here already which I would follow, but I also would expect to see differences (at least confounders like age, gender…
Comment: How to subset large BAM files specifically/ extract specific subsets?
by
GenoMax
134k
You may be able to do this by using the tool `reformat.sh` from BBTools without remapping. Can you try: reformat.sh in=your.bam out=f…
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